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(-) Description

Title :  CRYSTAL STRUCTURE OF HCV NS5B POLYMERASE IN COMPLEX WITH 2-{[(4-METHYLPHENYL)SULFONYL]AMINO}-5-PHENOXYBENZOIC ACID
 
Authors :  R. Coulombe
Date :  30 Jan 13  (Deposition) - 17 Apr 13  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna-Directed Rna Polymerase, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Stammers, R. Coulombe, J. Rancourt, B. Thavonekham, G. Fazal, S. Goulet, A. Jakalian, D. Wernic, Y. Tsantrizos, M. A. Poupart, M. Bos G. Mckercher, L. Thauvette, G. Kukolj, P. L. Beaulieu
Discovery Of A Novel Series Of Non-Nucleoside Thumb Pocket Hcv Ns5B Polymerase Inhibitors.
Bioorg. Med. Chem. Lett. V. 23 2585 2013
PubMed-ID: 23545108  |  Reference-DOI: 10.1016/J.BMCL.2013.02.110

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN
    Chains: A, B
    EC Number: 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RNA-DIRECTED RNA POLYMERASE, UNP RESIDUES 2420-2989
    Gene: NS5B
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 420174
    Other Details: PROTEIN CONSTRUCT ID 001
    Strain: 1BJ4
    Synonym: CORE PROTEIN P21, CAPSID PROTEIN C, P21, CORE PROTEIN P19, ENVELOPE GLYCOPROTEIN E1, GP32, GP35, ENVELOPE GLYCOPROTEIN E2, NS1, GP68, GP70, P7, PROTEASE NS2-3, P23, SERINE PROTEASE NS3, HEPACIVIRIN, NS3P, P70, NON-STRUCTURAL PROTEIN 4A, NS4A, P8, NON- STRUCTURAL PROTEIN 4B, NS4B, P27, NON-STRUCTURAL PROTEIN 5A, NS5A, P56, RNA-DIRECTED RNA POLYMERASE, NS5B, P68

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
11JH1Ligand/Ion2-{[(4-METHYLPHENYL)SULFONYL]AMINO}-5-PHENOXYBENZOICACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11JH1Ligand/Ion2-{[(4-METHYLPHENYL)SULFONYL]AMINO}-5-PHENOXYBENZOICACID
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
11JH-1Ligand/Ion2-{[(4-METHYLPHENYL)SULFONYL]AMINO}-5-PHENOXYBENZOICACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:422 , LEU A:474 , HIS A:475 , SER A:476 , TYR A:477 , ILE A:482 , LEU A:497 , TRP A:528 , HOH A:843BINDING SITE FOR RESIDUE 1JH A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J08)

(-) Exons   (0, 0)

(no "Exon" information available for 4J08)

(-) Sequences/Alignments

Asymmetric 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:559
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4j08a_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...................hhhhh..hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee........eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh.hhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j08 A   1 SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHS 563
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554         
                                                                                                                                                                              149|                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                               154                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:558
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4j08b_ B: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..................hhhhhh..hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh..hhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j08 B   1 SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHS 563
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555        
                                                                                                                                                                            147|                                                                                                                                                                                                                                                                                                                                                                                                                          
                                                                                                                                                                             153
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J08)

(-) Gene Ontology  (79, 79)

Asymmetric Unit(hide GO term definitions)

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  4j08
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        POLG_HCVJ4 | O92972: 1nb4 1nb6 1nb7 2f55 2mts 2xhu 2xhv 2xhw 2yoj 3cso 3gnv 3gnw 3gol 3hky 3lkh 3mwv 3mww 3ska 3ske 3skh 3tyq 3tyv 3u4o 3u4r 3uph 3upi 4dru 4eaw 4gmc 4iz0 4j02 4j04 4j06 4j0a 4jjs 4jju 4jtw 4jty 4jtz 4ju1 4ju2 4ju3 4ju4 4ju6 4ju7 4jvq 4jy0 4jy1 4mz4 4oow 4ry4 4ry5 4ry6 4ry7 5czb 5nph

(-) Related Entries Specified in the PDB File

3mwv HCV NS5B APO
4iz0 HCV NS5B WITH INHIBITOR 1
4j02
4j04
4j06
4j0a