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(-) Description

Title :  HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH A 2,6-DIFLUOROPHENYL DAPY ANALOG
 
Authors :  E. B. Lansdon
Date :  17 May 16  (Deposition) - 29 Jun 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-1, Reverse Transcriptase, Nnrti, Inhibitor Complex, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Simon, O. Baszczynski, D. Saman, G. Stepan, E. Hu, E. B. Lansdon, P. Jansa, Z. Janeba
Novel (2, 6-Difluorophenyl)(2-(Phenylamino)Pyrimidin-4-Yl) Methanones With Restricted Conformation As Potent Non-Nucleoside Reverse Transcriptase Inhibitors Against Hiv-1.
Eur. J. Med. Chem. V. 122 185 2016
PubMed-ID: 27371922  |  Reference-DOI: 10.1016/J.EJMECH.2016.06.026

(-) Compounds

Molecule 1 - HIV-1 REVERSE TRANSCRIPTASE(ISOLATE HXB2)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GAG-POL
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SUBTYPE B (ISOLATE HXB2)
    Organism Taxid: 11706
    Strain: ISOLATE HXB2
 
Molecule 2 - HIV-1 REVERSE TRANSCRIPTASE (ISOLATE LW123)
    Chains: B
    EC Number: 2.7.7.49
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GAG-POL
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SUBTYPE B (ISOLATE LW123)
    Organism Taxid: 82834
    Strain: ISOLATE LW123

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1IB11Ligand/Ion4-{[4-(2,6-DIFLUORO-4-METHOXYBENZENE-1-CARBONYL)PYRIMIDIN-2-YL]AMINO}BENZONITRILE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:95 , LEU A:100 , LYS A:101 , LYS A:103 , VAL A:106 , VAL A:179 , TYR A:181 , TYR A:188 , PHE A:227 , TRP A:229 , LEU A:234 , HIS A:235 , PRO A:236 , TYR A:318 , GLU B:138binding site for residue IB1 A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K14)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:225 -Pro A:226
2Pro A:345 -Phe A:346
3Pro A:420 -Pro A:421

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K14)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K14)

(-) Exons   (0, 0)

(no "Exon" information available for 5K14)

(-) 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:536
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhhh..eee..........eeee.....eeee.hhhhhhh............hhhhh....eeeeee...hhhhh..hhhhhhhhheee.hhhhh...eeeee........hhhhhhhhhhhhhhhhhhhh....eeeee..eeeeee..hhhhhhhhhhhhhhhhhh...........eee..eee....eee...........hhhhhhhhhhhhhhhh.......hhhhhhhhh...........hhhhhhhhhhhhhhhh..............eeeeee.....eeeeee.....eeeeeee......eehhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh........eee......................eeeeeeee......eeeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh...ee.hhhhhhhhhhhhhh.eeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k14 A   1 PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIG 543
                                    10        20        30        40        50        60   ||   73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   ||  227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537      
                                                                                          64|                                                                                                                                                  217|                                                                                                                                                                                                                                                                                                                                 
                                                                                           68                                                                                                                                                   222                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:401
                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhh..eee..........eeee......eeee.hhhhhhhhhhhhhh........hhhhh.eeeeee.hhhhhhh.....hhhhhheee.hhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeeee..hhhhhhhhhhhhhhhhhh.....ee..................hhhhhhhhhhhhhhhh.......hhhhhh..............hhhhhhhhhhhhhhh...............eeeeeeee..eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh........eee...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k14 B   6 ETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQL 429
                                    15        25        35        45        55        65|       77        87        97       107       117       127       137       147       157       167       177       187       197       207       233       243       253       263       273       283       293       303       313       323       333       343       353  ||   368       378       388       398       408       418       428 
                                                                                      65|                                                                                                                                                215|                                                                                                                         356|                                                                   
                                                                                       68                                                                                                                                                 232                                                                                                                          362
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5K14)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K14)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K14)

(-) Gene Ontology  (59, 104)

Asymmetric/Biological Unit(hide GO term definitions)

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  POL_HV1LW | P0C6F2
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  2.7.7.49
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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 5j2m 5j2n 5j2p 5j2q 5t82
        POL_HV1LW | P0C6F2: 3lp3 3th9 3vfa 4i8w 4i8z 4mc1 4mc2 4mc6 4mc9 4nyf 4qgi

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