Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 K103N MUTANT REVERSE TRANSCRIPTASE IN COMPLEX WITH GW564511.
 
Authors :  J. Ren, P. P. Chamberlain, D. K. Stammers
Date :  30 Jun 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-1 Reverse Transcriptase, Aids, Nnrti, Gw564511, Drug Resistance, K103N Mutation, Hydrolase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ren, P. P. Chamberlain, A. Stamp, S. A. Short, K. L. Weaver, K. R. Romines, R. Hazen, A. Freeman, R. G. Ferris, C. W. Andrews, L. Boone, J. H. Chan, D. K. Stammers
Structural Basis For The Improved Drug Resistance Profile Of New Generation Benzophenone Non-Nucleoside Hiv-1 Reverse Transcriptase Inhibitors.
J. Med. Chem. V. 51 5000 2008
PubMed-ID: 18665583  |  Reference-DOI: 10.1021/JM8004493
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REVERSE TRANSCRIPTASE/RIBONUCLEASE H
    Chains: A
    EC Number: 2.7.7.49, 2.7.7.7, 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK233-2
    Expression System Strain: HXB2
    Expression System Vector Type: PLASMID
    Fragment: GAG-POL POLYPROTEIN P66 SUBUNIT
    Gene: GAG-POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11706
    Strain: HXB2 ISOLATE
    Synonym: P66 RT
 
Molecule 2 - P51 RT
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK233-2
    Expression System Strain: DG2
    Expression System Vector Type: PLASMID
    Fragment: GAG-POL POLYPROTEIN P51 SUBUNIT
    Gene: GAG-POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11706
    Strain: HXB2 ISOLATE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CSD1Mod. Amino Acid3-SULFINOALANINE
2GWE1Ligand/IonN-{4-[AMINO(DIHYDROXY)-LAMBDA~4~-SULFANYL]-2-METHYLPHENYL}-2-(4-CHLORO-2-{[3-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]CARBONYL}PHENOXY)ACETAMIDE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:447 , ARG B:356 , ARG B:358 , GLY B:359 , HIS B:361BINDING SITE FOR RESIDUE PO4 B 1300
2AC2SOFTWAREGLY A:436 , ALA A:437 , ASN A:460BINDING SITE FOR RESIDUE PO4 A 1301
3AC3SOFTWAREPRO A:95 , LEU A:100 , LYS A:101 , LYS A:102 , ASN A:103 , SER A:105 , TYR A:181 , TYR A:188 , GLY A:190 , PRO A:225 , PHE A:227 , TRP A:229 , LEU A:234 , PRO A:236 , TYR A:318BINDING SITE FOR RESIDUE GWE A 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DM2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:225 -Pro A:226
2Pro A:420 -Pro A:421

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (82, 148)

Asymmetric/Biological Unit (82, 148)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_POL_HV1H2_069 *M628LPOL_HV1H2  ---  ---A/BM41L
02UniProtVAR_POL_HV1H2_070 *E631APOL_HV1H2  ---  ---A/BE44A
03UniProtVAR_POL_HV1H2_071 *E631DPOL_HV1H2  ---  ---A/BE44D
04UniProtVAR_POL_HV1H2_072 *P639RPOL_HV1H2  ---  ---A/BP52R
05UniProtVAR_POL_HV1H2_073 *N641DPOL_HV1H2  ---  ---A/BN54D
06UniProtVAR_POL_HV1H2_074 *A649VPOL_HV1H2  ---  ---A/BA62V
07UniProtVAR_POL_HV1H2_084 *T656APOL_HV1H2  ---  ---BT69A
08UniProtVAR_POL_HV1H2_085 *T656DPOL_HV1H2  ---  ---BT69D
09UniProtVAR_POL_HV1H2_086 *T656GPOL_HV1H2  ---  ---BT69G
10UniProtVAR_POL_HV1H2_087 *T656NPOL_HV1H2  ---  ---BT69N
11UniProtVAR_POL_HV1H2_088 *K657EPOL_HV1H2  ---  ---A/BK70E
12UniProtVAR_POL_HV1H2_089 *K657RPOL_HV1H2  ---  ---A/BK70R
13UniProtVAR_POL_HV1H2_090 *K657SPOL_HV1H2  ---  ---A/BK70S
14UniProtVAR_POL_HV1H2_091 *L661IPOL_HV1H2  ---  ---A/BL74I
15UniProtVAR_POL_HV1H2_092 *L661VPOL_HV1H2  ---  ---A/BL74V
16UniProtVAR_POL_HV1H2_093 *V662IPOL_HV1H2  ---  ---A/BV75I
17UniProtVAR_POL_HV1H2_094 *V662LPOL_HV1H2  ---  ---A/BV75L
18UniProtVAR_POL_HV1H2_095 *V662MPOL_HV1H2  ---  ---A/BV75M
19UniProtVAR_POL_HV1H2_096 *V662TPOL_HV1H2  ---  ---A/BV75T
20UniProtVAR_POL_HV1H2_097 *F664LPOL_HV1H2  ---  ---A/BF77L
21UniProtVAR_POL_HV1H2_098 *W675GPOL_HV1H2  ---  ---AW88G
22UniProtVAR_POL_HV1H2_099 *W675SPOL_HV1H2  ---  ---AW88S
23UniProtVAR_POL_HV1H2_100 *E676GPOL_HV1H2  ---  ---AE89G
24UniProtVAR_POL_HV1H2_101 *E676KPOL_HV1H2  ---  ---AE89K
25UniProtVAR_POL_HV1H2_102 *L679IPOL_HV1H2  ---  ---AL92I
26UniProtVAR_POL_HV1H2_103 *L687IPOL_HV1H2  ---  ---A/BL100I
27UniProtVAR_POL_HV1H2_104 *K688EPOL_HV1H2  ---  ---A/BK101E
28UniProtVAR_POL_HV1H2_105 *K688PPOL_HV1H2  ---  ---A/BK101P
29UniProtVAR_POL_HV1H2_106 *K688QPOL_HV1H2  ---  ---A/BK101Q
30UniProtVAR_POL_HV1H2_107 *K690EPOL_HV1H2  ---  ---A/BN103E
31UniProtVAR_POL_HV1H2_108 *K690NPOL_HV1H2  ---  ---A/BN103N
32UniProtVAR_POL_HV1H2_109 *K690RPOL_HV1H2  ---  ---A/BN103R
33UniProtVAR_POL_HV1H2_110 *V693APOL_HV1H2  ---  ---A/BV106A
34UniProtVAR_POL_HV1H2_111 *V693IPOL_HV1H2  ---  ---A/BV106I
35UniProtVAR_POL_HV1H2_112 *V693MPOL_HV1H2  ---  ---A/BV106M
36UniProtVAR_POL_HV1H2_113 *V695IPOL_HV1H2  ---  ---A/BV108I
37UniProtVAR_POL_HV1H2_114 *Y702FPOL_HV1H2  ---  ---A/BY115F
38UniProtVAR_POL_HV1H2_115 *F703YPOL_HV1H2  ---  ---A/BF116Y
39UniProtVAR_POL_HV1H2_116 *V705IPOL_HV1H2  ---  ---A/BV118I
40UniProtVAR_POL_HV1H2_117 *P706SPOL_HV1H2  ---  ---A/BP119S
41UniProtVAR_POL_HV1H2_118 *I722LPOL_HV1H2  ---  ---A/BI135L
42UniProtVAR_POL_HV1H2_119 *I722MPOL_HV1H2  ---  ---A/BI135M
43UniProtVAR_POL_HV1H2_120 *I722TPOL_HV1H2  ---  ---A/BI135T
44UniProtVAR_POL_HV1H2_121 *E725KPOL_HV1H2  ---  ---A/BE138K
45UniProtVAR_POL_HV1H2_122 *Q732MPOL_HV1H2  ---  ---A/BQ145M
46UniProtVAR_POL_HV1H2_123 *Q738MPOL_HV1H2  ---  ---A/BQ151M
47UniProtVAR_POL_HV1H2_124 *S743APOL_HV1H2  ---  ---A/BS156A
48UniProtVAR_POL_HV1H2_125 *P744SPOL_HV1H2  ---  ---A/BP157S
49UniProtVAR_POL_HV1H2_126 *Q748LPOL_HV1H2  ---  ---A/BQ161L
50UniProtVAR_POL_HV1H2_127 *V766DPOL_HV1H2  ---  ---A/BV179D
51UniProtVAR_POL_HV1H2_128 *Y768CPOL_HV1H2  ---  ---A/BY181C
52UniProtVAR_POL_HV1H2_129 *M771IPOL_HV1H2  ---  ---A/BM184I
53UniProtVAR_POL_HV1H2_130 *M771TPOL_HV1H2  ---  ---A/BM184T
54UniProtVAR_POL_HV1H2_131 *M771VPOL_HV1H2  ---  ---A/BM184V
55UniProtVAR_POL_HV1H2_132 *Y775CPOL_HV1H2  ---  ---A/BY188C
56UniProtVAR_POL_HV1H2_133 *Y775HPOL_HV1H2  ---  ---A/BY188H
57UniProtVAR_POL_HV1H2_134 *Y775LPOL_HV1H2  ---  ---A/BY188L
58UniProtVAR_POL_HV1H2_135 *V776IPOL_HV1H2  ---  ---A/BV189I
59UniProtVAR_POL_HV1H2_136 *G777APOL_HV1H2  ---  ---A/BG190A
60UniProtVAR_POL_HV1H2_137 *G777CPOL_HV1H2  ---  ---A/BG190C
61UniProtVAR_POL_HV1H2_138 *G777EPOL_HV1H2  ---  ---A/BG190E
62UniProtVAR_POL_HV1H2_139 *G777QPOL_HV1H2  ---  ---A/BG190Q
63UniProtVAR_POL_HV1H2_140 *G777SPOL_HV1H2  ---  ---A/BG190S
64UniProtVAR_POL_HV1H2_141 *G777TPOL_HV1H2  ---  ---A/BG190T
65UniProtVAR_POL_HV1H2_142 *G777VPOL_HV1H2  ---  ---A/BG190V
66UniProtVAR_POL_HV1H2_143 *H795YPOL_HV1H2  ---  ---A/BH208Y
67UniProtVAR_POL_HV1H2_144 *L797WPOL_HV1H2  ---  ---A/BL210W
68UniProtVAR_POL_HV1H2_145 *R798KPOL_HV1H2  ---  ---A/BR211K
69UniProtVAR_POL_HV1H2_146 *L801FPOL_HV1H2  ---  ---AL214F
70UniProtVAR_POL_HV1H2_147 *T802FPOL_HV1H2  ---  ---AT215F
71UniProtVAR_POL_HV1H2_148 *T802YPOL_HV1H2  ---  ---AT215Y
72UniProtVAR_POL_HV1H2_149 *K806EPOL_HV1H2  ---  ---AK219E
73UniProtVAR_POL_HV1H2_150 *K806QPOL_HV1H2  ---  ---AK219Q
74UniProtVAR_POL_HV1H2_151 *K806RPOL_HV1H2  ---  ---AK219R
75UniProtVAR_POL_HV1H2_152 *P812HPOL_HV1H2  ---  ---AP225H
76UniProtVAR_POL_HV1H2_153 *P823LPOL_HV1H2  ---  ---A/BP236L
77UniProtVAR_POL_HV1H2_154 *K825TPOL_HV1H2  ---  ---A/BK238T
78UniProtVAR_POL_HV1H2_155 *L870IPOL_HV1H2  ---  ---A/BL283I
79UniProtVAR_POL_HV1H2_156 *Y905FPOL_HV1H2  ---  ---A/BY318F
80UniProtVAR_POL_HV1H2_157 *G920DPOL_HV1H2  ---  ---A/BG333D
81UniProtVAR_POL_HV1H2_158 *G920EPOL_HV1H2  ---  ---A/BG333E
82UniProtVAR_POL_HV1H2_159 *T973IPOL_HV1H2  ---  ---A/BT386I
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RT_POLPS50878 Reverse transcriptase (RT) catalytic domain profile.POL_HV1H2631-821
 		  2A:44-234
B:44-234
2RNASE_HPS50879 RNase H domain profile.POL_HV1H21021-1144
 		  2A:434-539
B:434-437

(-) Exons   (0, 0)

(no "Exon" information available for 3DM2)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:532
 aligned with A7YKL0_9HIV1 | A7YKL0 from UniProtKB/TrEMBL  Length:1008

    Alignment length:539
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690         
        A7YKL0_9HIV1    161 PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICAEMEKEGKISKIGPENPYNTPVFAIRKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH  699
               SCOP domains d3dm2a1 A:1-429 HIV-1 reverse transcriptase                                                                                                                                                                                                                                                                                                                                                                                                  d3dm2a2 A:430-539 automated matches                                                                            SCOP domains
               CATH domains 3dm2A01 A:1-90,A:116-156 HIV Type 1 Reverse Transcriptase, subun     it A, domain 1       3dm2A02                  3dm2A01 A:1-90,A:116  -156               3dm2A02 A:91-115,A:157-225  [code=3.30.70.270, no name defined]      3dm2A03 A:226-319  [code=3.30.70.270, no name defined]                                        3dm2A04 A:320-426  [code=3.30.70.270, no name defined]                                                     3dm2A05 A:427-538  [code=3.30.420.10, no name defined]                                                          - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhhhh.eee..........eeee.-----..eeee.hhhhhhhh...........hhhhh....eeeeee.hhhh.....hhhhhhhhheee...--....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee..hhhhhhhhhhhhhhhhhh...............eee..eeee..eeee...........hhhhhhhhhhhhhhhhhhh....hhhhhhh.............hhhhhhhhhhhhhhh....ee.........eeeeeeee..eeeeeeeee..eeeeeeee......eehhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh..........eee.....................eeeeeeeeee....eeeeeeee....eeeeeee..hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh..ee.hhhhhhhhhhhhhh.eeeeee.... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------L--A-------R-D-------V-------E---II-L----------GG--I-------IE-E--A-I------FY-IS---------------L--K------M-----M----AS---L-----------------D-C--I---CIA-----------------Y-WK--FF---E-----H----------L-T--------------------------------------------I----------------------------------F--------------D----------------------------------------------------I--------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------D-------------------------R---VL------------SK-----------P-N--I----------------------------M------------------------------------------------T---H-C------------------------Y---Q-----------------------------------------------------------------------------------------------------------------E-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------S----M-------------------------Q-R--M----------------------------T------------------------------------------------V---L-E----------------------------R-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) --------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
             SAPs(SNPs) (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (5)
             SAPs(SNPs) (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (6)
             SAPs(SNPs) (7) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (7)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3dm2 A    1 PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIK-----KWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSI--ETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLcKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH  539
                                    10        20        30        40        50        60   |    70        80        90       100       110       120       130    |  140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530         
                                                                                          64    70                                                              135  |                                                                                                                                           280-CSD                                                                                                                                                                                                                                                               
                                                                                                                                                                   138                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain A from PDB  Type:PROTEIN  Length:532
 aligned with POL_HV1H2 | P04585 from UniProtKB/Swiss-Prot  Length:1435

    Alignment length:539
                                   597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117         
           POL_HV1H2    588 PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH 1126
               SCOP domains d3dm2a1 A:1-429 HIV-1 reverse transcriptase                                                                                                                                                                                                                                                                                                                                                                                                  d3dm2a2 A:430-539 automated matches                                                                            SCOP domains
               CATH domains 3dm2A01 A:1-90,A:116-156 HIV Type 1 Reverse Transcriptase, subun     it A, domain 1       3dm2A02                  3dm2A01 A:1-90,A:116  -156               3dm2A02 A:91-115,A:157-225  [code=3.30.70.270, no name defined]      3dm2A03 A:226-319  [code=3.30.70.270, no name defined]                                        3dm2A04 A:320-426  [code=3.30.70.270, no name defined]                                                     3dm2A05 A:427-538  [code=3.30.420.10, no name defined]                                                          - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhhhh.eee..........eeee.-----..eeee.hhhhhhhh...........hhhhh....eeeeee.hhhh.....hhhhhhhhheee...--....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee..hhhhhhhhhhhhhhhhhh...............eee..eeee..eeee...........hhhhhhhhhhhhhhhhhhh....hhhhhhh.............hhhhhhhhhhhhhhh....ee.........eeeeeeee..eeeeeeeee..eeeeeeee......eehhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh..........eee.....................eeeeeeeeee....eeeeeeee....eeeeeee..hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh..ee.hhhhhhhhhhhhhh.eeeeee.... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------L--A-------R-D-------V-------E---II-L----------GG--I-------IE-E--A-I------FY-IS---------------L--K------M-----M----AS---L-----------------D-C--I---CIA-----------------Y-WK--FF---E-----H----------L-T--------------------------------------------I----------------------------------F--------------D----------------------------------------------------I--------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------D-------------------------R---VL------------SK-----------P-N--I----------------------------M------------------------------------------------T---H-C------------------------Y---Q-----------------------------------------------------------------------------------------------------------------E-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------S----M-------------------------Q-R--M----------------------------T------------------------------------------------V---L-E----------------------------R-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) --------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
             SAPs(SNPs) (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (5)
             SAPs(SNPs) (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (6)
             SAPs(SNPs) (7) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (7)
                    PROSITE -------------------------------------------RT_POL  PDB: A:44-234 UniProt: 631-821                                                                                                                                                         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNASE_H  PDB: A:434-539 UniProt: 1021-1144                                                                 PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3dm2 A    1 PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIK-----KWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSI--ETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLcKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH  539
                                    10        20        30        40        50        60   |    70        80        90       100       110       120       130    |  140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530         
                                                                                          64    70                                                              135  |                                                                                                                                           280-CSD                                                                                                                                                                                                                                                               
                                                                                                                                                                   138                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:400
 aligned with POL_HV1H2 | P04585 from UniProtKB/Swiss-Prot  Length:1435

    Alignment length:431
                                   603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023 
           POL_HV1H2    594 TVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGA 1024
               SCOP domains d3dm2b_ B: HIV-1 reverse transcriptase                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3dm2B01 B:7-97,B:116-156 HIV Type 1 Reverse Transcriptase,     subunit A, domain        1  -3dm2B02          3dm2B01 B:7-97,B:116-156                 3dm2B02 B:99-115,B:157-238  [code=3.30.70.270, no name d                    efined3dm2B03 B:239-319  [code=3.30.70.270, no name defined]                           3dm2B04 B:320-426  [code=3.30.70.270, no name defined]                                                     ----------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhh..eee..........eeee.----...eeee.hhhhhhhh...-------....hhhhh.eeeeee.hhhhhhh.....hhhhhheee.hhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeeee..hhhhhhhhhhhhhhhhh..--------------------..hhhhh............eehhhhhhhhhhhhhhh.......hhhhhhhh........ee..hhhhhhhhhhhhhhh...............eeeeeeee..eeeeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh......eeee...hhhhhhhhh......... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------L--A-------R-D-------V------AE---II-L----------------------IE-E--A-I------FY-IS---------------L--K------M-----M----AS---L-----------------D-C--I---CIA-----------------Y-WK------------------------L-T--------------------------------------------I----------------------------------F--------------D----------------------------------------------------I--------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------D------------------------DR---VL-------------------------P-N--I----------------------------M------------------------------------------------T---H-C----------------------------------------------------------------------------------------------------------------------------------------------E-------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------------GS----M-------------------------Q-R--M----------------------------T------------------------------------------------V---L-E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) --------------------------------------------------------------N-----T------------------------------------------------------------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
             SAPs(SNPs) (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (5)
             SAPs(SNPs) (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (6)
             SAPs(SNPs) (7) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (7)
                    PROSITE -------------------------------------RT_POL  PDB: B:44-234 UniProt: 631-821                                                                                                                                                         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNAS PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3dm2 B    7 TVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIK----TKWRKLVDFRELNKRTQDF-------PHPAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRW--------------------ELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGA  437
                                    16        26        36        46        56       | -  |     76        86|       96       106       116       126       136       146       156       166       176       186       196       206     |   -         -      |236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436 
                                                                                    64   69                87      95                                                                                                                  212                  233                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:400
 aligned with Q74596_9HIV1 | Q74596 from UniProtKB/TrEMBL  Length:1015

    Alignment length:431
                                   183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603 
        Q74596_9HIV1    174 TVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGA  604
               SCOP domains d3dm2b_ B: HIV-1 reverse transcriptase                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3dm2B01 B:7-97,B:116-156 HIV Type 1 Reverse Transcriptase,     subunit A, domain        1  -3dm2B02          3dm2B01 B:7-97,B:116-156                 3dm2B02 B:99-115,B:157-238  [code=3.30.70.270, no name d                    efined3dm2B03 B:239-319  [code=3.30.70.270, no name defined]                           3dm2B04 B:320-426  [code=3.30.70.270, no name defined]                                                     ----------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhh..eee..........eeee.----...eeee.hhhhhhhh...-------....hhhhh.eeeeee.hhhhhhh.....hhhhhheee.hhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeeee..hhhhhhhhhhhhhhhhh..--------------------..hhhhh............eehhhhhhhhhhhhhhh.......hhhhhhhh........ee..hhhhhhhhhhhhhhh...............eeeeeeee..eeeeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh......eeee...hhhhhhhhh......... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------L--A-------R-D-------V------AE---II-L----------------------IE-E--A-I------FY-IS---------------L--K------M-----M----AS---L-----------------D-C--I---CIA-----------------Y-WK------------------------L-T--------------------------------------------I----------------------------------F--------------D----------------------------------------------------I--------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------D------------------------DR---VL-------------------------P-N--I----------------------------M------------------------------------------------T---H-C----------------------------------------------------------------------------------------------------------------------------------------------E-------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------------GS----M-------------------------Q-R--M----------------------------T------------------------------------------------V---L-E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) --------------------------------------------------------------N-----T------------------------------------------------------------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
             SAPs(SNPs) (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (5)
             SAPs(SNPs) (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (6)
             SAPs(SNPs) (7) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (7)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3dm2 B    7 TVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIK----TKWRKLVDFRELNKRTQDF-------PHPAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRW--------------------ELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGA  437
                                    16        26        36        46        56       | -  |     76        86|       96       106       116       126       136       146       156       166       176       186       196       206     |   -         -      |236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436 
                                                                                    64   69                87      95                                                                                                                  212                  233
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (3, 9)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DM2)

(-) Gene Ontology  (59, 105)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A7YKL0_9HIV1 | A7YKL0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.

Chain A,B   (POL_HV1H2 | P04585)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004533    exoribonuclease H activity    Catalysis of the exonucleolytic cleavage of RNA to 5'-phosphomonoester oligonucleotides in both 5' to 3' and 3' to 5' directions.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008907    integrase activity    Catalysis of the integration of one segment of DNA into another.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0030260    entry into host cell    The invasion by an organism of a cell of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0039526    modulation by virus of host apoptotic process    Any process in which a virus modulates the frequency, rate or extent of apoptosis of infected host cells.
    GO:0051169    nuclear transport    The directed movement of substances into, out of, or within the nucleus.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0019061    uncoating of virus    The process by which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019072    viral genome packaging    The encapsulation of the viral genome within the capsid.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    GO:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
    GO:0019068    virion assembly    A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0072494    host multivesicular body    A late endosome in which regions of the limiting host cell endosomal membrane invaginate to form internal vesicles; host membrane proteins that enter the internal vesicles are sequestered from the host cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

Chain B   (Q74596_9HIV1 | Q74596)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CSD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GWE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:225 - Pro A:226   [ RasMol ]  
    Pro A:420 - Pro A:421   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3dm2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A7YKL0_9HIV1 | A7YKL0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  POL_HV1H2 | P04585
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q74596_9HIV1 | Q74596
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.49
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.7.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.1.26.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  A7YKL0_9HIV1 | A7YKL0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  POL_HV1H2 | P04585
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q74596_9HIV1 | Q74596
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        POL_HV1H2 | P04585: 1a30 1bv7 1bv9 1bve 1bvg 1bwa 1bwb 1c0t 1c0u 1c1b 1c1c 1dmp 1dtq 1dtt 1e6j 1ep4 1esk 1ex4 1exq 1fb7 1fk9 1fko 1fkp 1g6l 1hiv 1hvh 1hvr 1hwr 1hxb 1jkh 1jla 1jlb 1jlc 1jle 1jlf 1jlg 1jlq 1klm 1lv1 1lw0 1lw2 1lwc 1lwe 1lwf 1ncp 1o1w 1odw 1odx 1ody 1qbr 1qbs 1qbt 1qbu 1rev 1rt1 1rt2 1rt3 1rt4 1rt5 1rt6 1rt7 1rtd 1rth 1rti 1rtj 1s1t 1s1u 1s1v 1s1w 1s1x 1t05 1tam 1tkt 1tkx 1tkz 1tl1 1tl3 1vrt 1vru 2hnd 2hny 2hnz 2kod 2nph 2opp 2opq 2opr 2ops 2rf2 2rki 2whh 2wom 2won 2ynf 2yng 2ynh 2yni 3ao2 3c6t 3c6u 3di6 3dle 3dlg 3dmj 3dok 3dol 3dox 3drp 3drr 3drs 3dya 3e01 3ffi 3i0r 3i0s 3kjv 3kk1 3kk2 3kk3 3kt2 3kt5 3lak 3lal 3lam 3lan 3lp0 3lp1 3lp2 3m8p 3m8q 3mec 3med 3mee 3meg 3mim 3n3i 3nbp 3phv 3qin 3qio 3qip 3t19 3t1a 3tam 4b3o 4b3p 4b3q 4i7f 4kse 4kv8 4ncg 4q1w 4q1x 4q1y 4q5m 4qlh 4u1h 4u1i 4u1j 4u7q 4u7v 5dgu 5dgw 5eu7 5hrn 5hrp 5hrr 5hrs 5im7 5j2m 5j2n 5j2p 5j2q 5k14 5t82
        Q74596_9HIV1 | Q74596: 5t82
UniProtKB/TrEMBL
        A7YKL0_9HIV1 | A7YKL0: 3dmj 3dok 3dol
        Q74596_9HIV1 | Q74596: 3dmj

(-) Related Entries Specified in the PDB File

3dle CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH GF128590
3dlg CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH GW564511