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(-) Description

Title :  CRYSTAL STRUCTURE OF HCV NS5B POLYMERASE IN COMPLEX WITH A THUMB INHIBITOR
 
Authors :  R. Coulombe
Date :  15 Aug 12  (Deposition) - 20 Feb 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. L. Beaulieu, R. Coulombe, J. Gillard, C. Brochu, J. Duan, M. Garneau E. Jolicoeur, P. Kuhn, M. A. Poupart, J. Rancourt, T. A. Stammers, B. Thavonekham, G. Kukolj
Allosteric N-Acetamide-Indole-6-Carboxylic Acid Thumb Pocke 1 Inhibitors Of Hepatitis C Virus Ns5B Polymerase - Acylsulfonamides And Acylsulfamides As Carboxylic Acid Replacements
Can. J. Chem. V. 91 66 2013
PubMed: search  |  Reference-DOI: 10.1139/CJC-2012-0319

(-) Compounds

Molecule 1 - NS5B POLYMERASE
    Chains: A, B
    EC Number: 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: UNP RESIDUES 2420-2989
    Gene: NS5B
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 420174
    Strain: HC-J4
    Synonym: RNA-DIRECTED RNA POLYMERASE

 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  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
11BI1Ligand/Ion3-CYCLOHEXYL-2-(FURAN-3-YL)-1-[2-(MORPHOLIN-4-YL)-2-OXOETHYL]-N-(PHENYLSULFONYL)-1H-INDOLE-6-CARBOXAMIDE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
11BI-1Ligand/Ion3-CYCLOHEXYL-2-(FURAN-3-YL)-1-[2-(MORPHOLIN-4-YL)-2-OXOETHYL]-N-(PHENYLSULFONYL)-1H-INDOLE-6-CARBOXAMIDE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
11BI1Ligand/Ion3-CYCLOHEXYL-2-(FURAN-3-YL)-1-[2-(MORPHOLIN-4-YL)-2-OXOETHYL]-N-(PHENYLSULFONYL)-1H-INDOLE-6-CARBOXAMIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:48 , LYS A:51 , ARG A:158 , THR A:221 , CYS A:223BINDING SITE FOR RESIDUE SO4 A 601
2AC2SOFTWAREASN A:291 , GLY A:317 , ASP A:318 , SER A:556BINDING SITE FOR RESIDUE SO4 A 602
3AC3SOFTWAREVAL B:37 , ALA B:393 , ALA B:396 , HIS B:428 , LEU B:492 , GLY B:493 , VAL B:494 , ARG B:503BINDING SITE FOR RESIDUE 1BI B 601
4AC4SOFTWAREARG B:48 , LYS B:51 , ARG B:158 , THR B:221 , CYS B:223BINDING SITE FOR RESIDUE SO4 B 602
5AC5SOFTWAREPHE B:193 , SER B:288 , ASN B:291 , GLY B:317 , ASP B:318 , SER B:556BINDING SITE FOR RESIDUE SO4 B 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GMC)

(-) 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 d4gmca_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhh...hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gmc 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:541
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4gmcb_ B: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee............eee....hhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eee...........eee..hhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhhhh..........ee..ee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gmc B   1 SMSYTWTGALITPCAAEMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHS 563
                                    10      ||38        48        58        68        78        88        98       108       118       128       138       148|      162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562 
                                           17|                                                                                                             148|                                                                                                                                                                                                                                                                                                                                                                                                                          
                                            36                                                                                                              153
   Legend:   → Mismatch (orange background)
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (79, 79)

Asymmetric Unit(hide GO term definitions)

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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 4iz0 4j02 4j04 4j06 4j08 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 APO NS5B POLYMERASE
3mww NS5B POLYMERASE IN COMPLEX WITH AN INHIBITOR