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(-) Description

Title :  HCV NS5B GT1A WITH GSK5852
 
Authors :  S. P. Williams, K. M. Kahler, J. B. Shotwell
Date :  30 Apr 13  (Deposition) - 15 May 13  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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, 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 - HCV 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 POLYMERASE 1-571, UNP RESIDUES 2421-2990
    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, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
11PV2Ligand/Ion[4-({[5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-6-YL](METHYLSULFONYL)AMINO}METHYL)-2-FLUOROPHENYL]BORONIC ACID
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
11PV1Ligand/Ion[4-({[5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-6-YL](METHYLSULFONYL)AMINO}METHYL)-2-FLUOROPHENYL]BORONIC ACID
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
11PV1Ligand/Ion[4-({[5-CYCLOPROPYL-2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-6-YL](METHYLSULFONYL)AMINO}METHYL)-2-FLUOROPHENYL]BORONIC ACID
2SO45Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:193 , ARG A:200 , LEU A:204 , LEU A:314 , CYS A:316 , ILE A:363 , SER A:365 , CYS A:366 , SER A:368 , MET A:414 , TYR A:448 , HOH A:1154BINDING SITE FOR RESIDUE 1PV A 601
2AC2SOFTWAREARG A:505 , ARG A:531 , THR A:532BINDING SITE FOR RESIDUE SO4 A 602
3AC3SOFTWAREARG A:48 , LYS A:51 , ARG A:222 , CYS A:223 , HOH A:790BINDING SITE FOR RESIDUE SO4 A 603
4AC4SOFTWAREPHE B:193 , ARG B:200 , LEU B:204 , LEU B:314 , CYS B:316 , ASP B:319 , VAL B:321 , ILE B:363 , SER B:365 , CYS B:366 , SER B:368 , MET B:414 , TYR B:448 , HOH B:900 , HOH B:1153BINDING SITE FOR RESIDUE 1PV B 601
5AC5SOFTWAREASN A:24 , LEU A:26 , ARG A:436 , LYS B:209 , ARG B:380 , TYR B:382 , HOH B:724BINDING SITE FOR RESIDUE SO4 B 602
6AC6SOFTWAREARG B:48 , LYS B:51 , ARG B:222 , CYS B:223BINDING SITE FOR RESIDUE SO4 B 603
7AC7SOFTWAREASN B:24 , LEU B:26 , ARG B:436 , HOH B:965BINDING SITE FOR RESIDUE SO4 B 604
8AC8SOFTWAREGLY B:516 , ARG B:517 , HOH B:785BINDING SITE FOR RESIDUE SO4 B 605
9AC9SOFTWAREARG B:505 , ARG B:531 , THR B:532 , HOH B:1134BINDING SITE FOR RESIDUE SO4 B 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KHM)

(-) 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 d4khma_ 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.hhhhh......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh.hhhhhh........ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4khm A   1 SMSYSWTGALVTPCAAEEQKLPINALSNSLLRHHNLVYSTTSRSACQRQKKVTFDRLQVLDSHYQDVLKEVKAAASKVKANLLSVEEACSLTPPHSAKSKYGYGAKDVRSHASRAVAHINSVWKDLLEDSVTPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSKLPLAVMGSSYGFQYSPGQRVEFLVQAWKSKKTPMGFSYDTRCFDSTVTESDIRTEEAIYQCCDLDPQARVAIKSLTERLYVGGPLTNSRGENCGYRRCRASGVLTTSCGNTLTCYIKARAACRAAGLQDCTMLVCGDDLVVICESAGVQEDAASLRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDGAGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMFAPTLWARMILMTHFFSVLIARDQLEQALDCEIYGACYSIEPLDLPPIIQRLHGLSAFSLHSYSPGEINRVAACLRKLGVPPLRAWRHRARSVRARLLSRGGRAAICGKYLFNWAVRTKLKLTPIAAAGQLALSGWFTAGYSGGDIYH 562
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Chain B from PDB  Type:PROTEIN  Length:562
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4khmb_ 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......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh...............ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4khm B   1 SMSYSWTGALVTPCAAEEQKLPINALSNSLLRHHNLVYSTTSRSACQRQKKVTFDRLQVLDSHYQDVLKEVKAAASKVKANLLSVEEACSLTPPHSAKSKYGYGAKDVRSHASRAVAHINSVWKDLLEDSVTPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSKLPLAVMGSSYGFQYSPGQRVEFLVQAWKSKKTPMGFSYDTRCFDSTVTESDIRTEEAIYQCCDLDPQARVAIKSLTERLYVGGPLTNSRGENCGYRRCRASGVLTTSCGNTLTCYIKARAACRAAGLQDCTMLVCGDDLVVICESAGVQEDAASLRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDGAGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMFAPTLWARMILMTHFFSVLIARDQLEQALDCEIYGACYSIEPLDLPPIIQRLHGLSAFSLHSYSPGEINRVAACLRKLGVPPLRAWRHRARSVRARLLSRGGRAAICGKYLFNWAVRTKLKLTPIAAAGQLALSGWFTAGYSGGDIYH 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)
  - → 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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        B1PPP0_9HEPC | B1PPP0: 4khr

(-) Related Entries Specified in the PDB File

4kai HCV NS5B GT1B N316 WITH GSK5852A
4kb7 HCV NS5B GT1B N316Y WITH CMPD 32
4kbi HCV NS5B GT1B N316Y WITH CMPD 4
4ke5 HCV NS5B GT1B N316Y WITH GSK5852
4khr 'HCV NS5B GT1A C316Y WITH GSK5852