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(-) Description

Title :  HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH DNA AND EFDA-TRIPHOSPHATE, A TRANSLOCATION-DEFECTIVE RT INHIBITOR
 
Authors :  Z. L. Salie, K. A. Kirby, S. G. Sarafianos
Date :  29 Mar 16  (Deposition) - 03 Aug 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.43
Chains :  Asym./Biol. Unit :  A,B,P,T
Keywords :  Hiv-1, Reverse Transcriptase, Rt, Dna, Double Stranded Dna, Dsdna, Efda, 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine, Efda-Triphosphate, Efda-Tp, Inhibitors, Nrti, Tdrti, Translocation Defective, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. L. Salie, K. A. Kirby, E. Michailidis, B. Marchand, K. Singh, L. C. Rohan, E. N. Kodama, H. Mitsuya, M. A. Parniak, S. G. Sarafianos
Structural Basis Of Hiv Inhibition By Translocation-Defective Rt Inhibitor 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine (Efda).
Proc. Natl. Acad. Sci. Usa V. 113 9274 2016
PubMed-ID: 27489345  |  Reference-DOI: 10.1073/PNAS.1605223113

(-) Compounds

Molecule 1 - HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
    Chains: A
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDFDUET1
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-560
    Gene: GAG-POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SUBTYPE B (ISOLATE HXB2)
    Organism Taxid: 11706
    Strain: ISOLATE HXB2
    Synonym: PR160GAG-POL
 
Molecule 2 - HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
    Chains: B
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET1
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-440
    Gene: GAG-POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SUBTYPE B (ISOLATE HXB2)
    Organism Taxid: 11706
    Strain: ISOLATE HXB2
    Synonym: PR160GAG-POL
 
Molecule 3 - DNA (5'- D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*G)-3')
    Chains: P
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synthetic: YES
 
Molecule 4 - DNA (27-MER)
    Chains: T
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
16FN1Ligand/Ion2'-DEOXY-4'-ETHYNYL-2-FLUOROADENOSINE 5'-(TETRAHYDROGENTRIPHOSPHATE)
2MG3Ligand/IonMAGNESIUM ION
3MRG1Mod. NucleotideN2-(3-MERCAPTOPROPYL)-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:110 , VAL A:111 , ASP A:185binding site for residue MG A 601
2AC2SOFTWAREASP A:443 , GLU A:478 , ASP A:498 , HOH A:723 , HOH A:729 , HOH A:738binding site for residue MG A 602
3AC3SOFTWAREASP A:110 , ASP A:185 , HOH A:816 , DG P:822binding site for residue MG A 603

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:258 -P:817

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:225 -Pro A:226
2Pro A:420 -Pro A:421
3Gly A:543 -Gly A:544
4Gly B:213 -Leu B:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J2M)

(-) Exons   (0, 0)

(no "Exon" information available for 5J2M)

(-) 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:558
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhhh..eee..........eeeee......eeeee.hhhhhhhh...........hhhhh....eeeeee...hhhhh..hhhhhhhhheee.........eeeee........hhhhhhhhhhhhhhhhhhhhh...eeeee..eeeeee..hhhhhhhhhhhhhhhhhhh....hhhhh.....eee..eee....eee...........hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhhhhhhhhhhh..............eeeeeee...eeeeeeeee..eeeeeeee......eehhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh........eee.....................eeeeeeeee......eeeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh...ee.hhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j2m A   1 PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDICKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK 558
                                    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       540       550        


Chain B from PDB  Type:PROTEIN  Length:398
                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhhhhh..eeee.........eeeee......eeeee.hhhhhhhh.hhhhhhh.eeeeee.hhhhhhh..hhhhhhhhheee.hhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeeee....hhhhhhhhhhhhhhhh.....hhhhh............eehhhhhhhhhhhhhhh.......hhhhhhhhh.......ee..hhhhhhhhhhhhhhhhh.............eeeeeeee..eeeeeee.....eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh........eee...hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j2m B   4 PIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLE 430
                                    13        23        33        43        53        63        73        83||     104       114       124       134       144       154       164       174       184       194       204       214|      242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422        
                                                                                                           84|                                                                                                                   214|                                                                                                                                                                                                     
                                                                                                            96                                                                                                                    233                                                                                                                                                                                                     


Chain P from PDB  Type:DNA  Length:18
                                                  
                 5j2m P 805 GTCCCTGTTCGGxCGCCG 822
                                   814  |     
                                      817-MRG 


Chain T from PDB  Type:DNA  Length:24
                                                        
                 5j2m T 702 TGGTCGGCGCCCGAACAGGGACTG 725
                                   711       721
   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  (0, 0)

(no "SCOP Domain" information available for 5J2M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J2M)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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    Pro A:420 - Pro A:421   [ RasMol ]  
 

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  5j2m
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  POL_HV1H2 | P04585
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 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 3dm2 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 5j2n 5j2p 5j2q 5k14 5t82

(-) Related Entries Specified in the PDB File

5j2n 5j2p 5j2q