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(-) Description

Title :  HCV NS5B GT1A C316Y WITH GSK5852
 
Authors :  S. P. Williams, K. M. Kahler, J. B. Shotwell
Date :  01 May 13  (Deposition) - 29 May 13  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hcv Polymerase, Hcv Ns5B, Site Iv Inhibitor, Boron, P66, P70, Rna Dependent Rna Polymerase, Rna Directed Rna Polymerase, Polymerase, Rns Dependent Rna Polymerase, Replication-Replication Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Maynard, R. M. Crosby, B. Ellis, R. Hamatake, Z. Hong, B. A. Johns, K. M. Kahler, C. Koble, A. Leivers, M. R. Leivers, A. Mathis, A. J. Peat, J. J. Pouliot, C. D. Roberts, V. Samano, R. M. Schmidt, G. K. Smith, A. Spaltenstein, E. L. Stewart, P. Thommes, E. M. Turner, C. Voitenleitner, J. T. Walker, G. Waitt, J. Weatherhead, K. Weaver, S. Williams, L. Wright, Z. Z. Xiong, D. Haigh, J. B. Shotwell
Discovery Of A Potent Boronic Acid Derived Inhibitor Of The Hcv Rna-Dependent Rna Polymerase.
J. Med. Chem. V. 57 1902 2014
PubMed-ID: 23672667  |  Reference-DOI: 10.1021/JM400317W

(-) Compounds

Molecule 1 - NS5B RNA-DEPENDENT RNA POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HCV NS5B GT1A C316Y 1-571
    Gene: NS5B
    Mutation: YES
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS SUBTYPE 1A
    Organism Taxid: 31646
    Strain: GENOTYPE 1A
    Synonym: 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  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
11PV1Ligand/Ion[4-({[5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-6-YL](METHYLSULFONYL)AMINO}METHYL)-2-FLUOROPHENYL]BORONIC ACID
2SO410Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
11PV1Ligand/Ion[4-({[5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-6-YL](METHYLSULFONYL)AMINO}METHYL)-2-FLUOROPHENYL]BORONIC ACID
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
11PV-1Ligand/Ion[4-({[5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-6-YL](METHYLSULFONYL)AMINO}METHYL)-2-FLUOROPHENYL]BORONIC ACID
2SO47Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:505 , VAL A:530 , ARG A:531 , THR A:532BINDING SITE FOR RESIDUE SO4 A 601
02AC2SOFTWAREGLY A:516 , ARG A:517BINDING SITE FOR RESIDUE SO4 A 602
03AC3SOFTWAREARG A:48 , LYS A:51 , THR A:221 , ARG A:222 , CYS A:223BINDING SITE FOR RESIDUE SO4 A 603
04AC4SOFTWAREPRO A:197 , ARG A:200 , LEU A:204 , LEU A:314 , TYR A:316 , ASP A:319 , VAL A:321 , ILE A:363 , SER A:365 , CYS A:366 , SER A:368 , MET A:414 , PHE A:415 , TYR A:448BINDING SITE FOR RESIDUE 1PV A 604
05AC5SOFTWAREASN A:24 , LEU A:26 , ARG A:436 , LYS B:209 , ARG B:380 , TYR B:382BINDING SITE FOR RESIDUE SO4 B 601
06AC6SOFTWAREASP A:437 , GLN A:438 , LEU A:439 , ARG A:514 , HOH A:721 , ASP B:359 , HOH B:748BINDING SITE FOR RESIDUE SO4 B 602
07AC7SOFTWAREGLY B:516 , ARG B:517BINDING SITE FOR RESIDUE SO4 B 603
08AC8SOFTWAREASN B:24 , LEU B:26 , ARG B:436BINDING SITE FOR RESIDUE SO4 B 604
09AC9SOFTWAREARG B:48 , LYS B:51 , ARG B:222 , CYS B:223BINDING SITE FOR RESIDUE SO4 B 605
10BC1SOFTWARESER B:96 , ALA B:97 , ARG B:168 , ASP B:559BINDING SITE FOR RESIDUE SO4 B 606
11BC2SOFTWAREARG B:505 , ARG B:531 , THR B:532BINDING SITE FOR RESIDUE SO4 B 607

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KHR)

(-) 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:562
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4khra_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhhhh.hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee............eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh...eee......hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhh..hhhhhh........ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4khr A   1 SMSYSWTGALVTPCAAEEQKLPINALSNSLLRHHNLVYSTTSRSACQRQKKVTFDRLQVLDSHYQDVLKEVKAAASKVKANLLSVEEACSLTPPHSAKSKYGYGAKDVRSHASRAVAHINSVWKDLLEDSVTPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSKLPLAVMGSSYGFQYSPGQRVEFLVQAWKSKKTPMGFSYDTRCFDSTVTESDIRTEEAIYQCCDLDPQARVAIKSLTERLYVGGPLTNSRGENCGYRRCRASGVLTTSCGNTLTCYIKARAACRAAGLQDCTMLVYGDDLVVICESAGVQEDAASLRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDGAGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMFAPTLWARMILMTHFFSVLIARDQLEQALDCEIYGACYSIEPLDLPPIIQRLHGLSAFSLHSYSPGEINRVAACLRKLGVPPLRAWRHRARSVRARLLSRGGRAAICGKYLFNWAVRTKLKLTPIAAAGQLALSGWFTAGYSGGDIYH 562
                                    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       560  


Chain B from PDB  Type:PROTEIN  Length:562
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4khrb_ B: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhhhh.hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee.hhhhh......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh...eee......hhhh.ee..eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhh................ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4khr B   1 SMSYSWTGALVTPCAAEEQKLPINALSNSLLRHHNLVYSTTSRSACQRQKKVTFDRLQVLDSHYQDVLKEVKAAASKVKANLLSVEEACSLTPPHSAKSKYGYGAKDVRSHASRAVAHINSVWKDLLEDSVTPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSKLPLAVMGSSYGFQYSPGQRVEFLVQAWKSKKTPMGFSYDTRCFDSTVTESDIRTEEAIYQCCDLDPQARVAIKSLTERLYVGGPLTNSRGENCGYRRCRASGVLTTSCGNTLTCYIKARAACRAAGLQDCTMLVYGDDLVVICESAGVQEDAASLRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDGAGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMFAPTLWARMILMTHFFSVLIARDQLEQALDCEIYGACYSIEPLDLPPIIQRLHGLSAFSLHSYSPGEINRVAACLRKLGVPPLRAWRHRARSVRARLLSRGGRAAICGKYLFNWAVRTKLKLTPIAAAGQLALSGWFTAGYSGGDIYH 562
                                    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       560
   Legend:   → Mismatch (orange background)
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    → 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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        B1PPP0_9HEPC | B1PPP0: 4khm

(-) Related Entries Specified in the PDB File

4kai HCV NS5B GT1B N316 WITH GSK5852
4kb7 HCV NS5B GT1B N316Y WITH CMPD 32
4kbi HCV NS5B GT1B N316Y WITH CMPD 4
4ke5 HCV NS5B GT1B N316Y WITH GSK5852
4khm HCV NS5B GT1A C316 WITH GSK5852