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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 3-[2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-5-YL]BENZOIC ACID
 
Authors :  S. Sheriff
Date :  27 Feb 17  (Deposition) - 10 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.54
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ns5B, Polymerase, Hcv, Fingers, Palm, Thumb, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. S. Yeung, B. R. Beno, K. Parcella, J. A. Bender, K. A. Grant-Young, A. Nickel, P. Gunaga, P. Anjanappa, R. O. Bora, K. Selvakumar, K. Rigat Y. K. Wang, M. Liu, J. Lemm, K. Mosure, S. Sheriff, C. Wan, M. Witmer, K. Kish, U. Hanumegowda, X. Zhuo, Y. Z. Shu, D. Parker, R. Haskell, A. Ng Q. Gao, E. Colston, J. Raybon, D. M. Grasela, K. Santone, M. Gao, N. A. Meanwell, M. Sinz, M. G. Soars, J. O. Knipe, S. B. Roberts, J. F. Kadow
Discovery Of A Hepatitis C Virus Ns5B Replicase Palm Site Allosteric Inhibitor (Bms-929075) Advanced To Phase 1 Clinical Studies.
J. Med. Chem. V. 60 4369 2017
PubMed-ID: 28430437  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00328

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS GENOTYPE 1B (ISOLATE CON1)
    Organism Taxid: 333284
    Strain: ISOLATE CON1

 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  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
123E2Ligand/Ion(2E)-3-(4-{[(1-{[(13-CYCLOHEXYL-6-OXO-6,7-DIHYDRO-5H-INDOLO[1,2-D][1,4]BENZODIAZEPIN-10-YL)CARBONYL]AMINO}CYCLOPENTYL)CARBONYL]AMINO}PHENYL)PROP-2-ENOIC ACID
28XS1Ligand/Ion3-[2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-5-YL]BENZOIC ACID
3GOL1Ligand/IonGLYCEROL
4SO410Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
123E1Ligand/Ion(2E)-3-(4-{[(1-{[(13-CYCLOHEXYL-6-OXO-6,7-DIHYDRO-5H-INDOLO[1,2-D][1,4]BENZODIAZEPIN-10-YL)CARBONYL]AMINO}CYCLOPENTYL)CARBONYL]AMINO}PHENYL)PROP-2-ENOIC ACID
28XS-1Ligand/Ion3-[2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-5-YL]BENZOIC ACID
3GOL-1Ligand/IonGLYCEROL
4SO45Ligand/IonSULFATE ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
123E1Ligand/Ion(2E)-3-(4-{[(1-{[(13-CYCLOHEXYL-6-OXO-6,7-DIHYDRO-5H-INDOLO[1,2-D][1,4]BENZODIAZEPIN-10-YL)CARBONYL]AMINO}CYCLOPENTYL)CARBONYL]AMINO}PHENYL)PROP-2-ENOIC ACID
28XS1Ligand/Ion3-[2-(4-FLUOROPHENYL)-3-(METHYLCARBAMOYL)-1-BENZOFURAN-5-YL]BENZOIC ACID
3GOL1Ligand/IonGLYCEROL
4SO45Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:392 , ALA A:396 , HIS A:428 , LEU A:492 , GLY A:493 , VAL A:494 , PRO A:495 , ARG A:498 , VAL A:499 , ARG A:503 , 23E B:601 , HOH B:748binding site for residue 23E A 601
02AC2SOFTWARESER A:84 , VAL A:85 , GLU A:86 , ARG A:120 , HOH A:763binding site for residue SO4 A 602
03AC3SOFTWAREARG A:48 , LYS A:51 , ARG A:222 , CYS A:223 , HOH A:743binding site for residue SO4 A 603
04AC4SOFTWAREHIS A:374 , SER A:476 , GLY A:516 , ARG A:517 , HOH A:756binding site for residue SO4 A 604
05AC5SOFTWAREPRO A:496 , LEU A:497 , ARG A:498 , ARG A:570 , HOH A:783binding site for residue SO4 A 605
06AC6SOFTWAREGLU A:361 , SER A:371 , SER A:478 , LYS A:523 , HOH A:771binding site for residue SO4 A 606
07AC7SOFTWAREALA A:400 , ARG A:401 , HIS A:428 , 23E A:601 , LEU B:392 , ALA B:396 , HIS B:428 , LEU B:492 , GLY B:493 , VAL B:494 , PRO B:495 , ARG B:498 , VAL B:499 , ARG B:503 , HOH B:748 , HOH B:773 , HOH B:789binding site for residue 23E B 601
08AC8SOFTWAREARG 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 , LEU B:384 , MET B:414 , TYR B:448 , HOH B:728binding site for residue 8XS B 602
09AC9SOFTWARESER B:84 , VAL B:85 , GLU B:86 , ARG B:120binding site for residue SO4 B 603
10AD1SOFTWAREGLY B:516 , ARG B:517 , HOH B:752binding site for residue SO4 B 604
11AD2SOFTWARESER A:1 , LYS B:379 , ARG B:380binding site for residue SO4 B 605
12AD3SOFTWAREHIS B:475 , SER B:476 , HOH B:759binding site for residue SO4 B 606
13AD4SOFTWAREARG B:48 , LYS B:51 , ARG B:158 , THR B:221 , ARG B:222 , CYS B:223binding site for residue SO4 B 607
14AD5SOFTWAREASN B:406 , TRP B:408 , LEU B:433 , GLN B:436binding site for residue GOL B 608

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5PZM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5PZM)

(-) 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:551
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.........ee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee.............eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh............hhhhh.ee..............eee.ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pzm A   1 SMSYTWTGALITPCVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSLSRARPRWFM 573
                                    10   ||   42        52        62        72        82        92       102       112       122       132       142       152       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       572 
                                        14|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                         37                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:545
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.........ee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...ee.............eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh............hhhhh.................eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pzm B   1 SMSYTWTGALITPCVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSLSRA 567
                                    10   ||   42        52        62        72        82        92       102       112       122       132       142       152       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     
                                        14|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                         37
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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  (0, 0)

(no "SCOP Domain" information available for 5PZM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 74)

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  5pzm
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  POLG_HCVCO | Q9WMX2
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  2.7.7.48
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_HCVCO | Q9WMX2: 1zh1 2jy0 2kwt 2kwz 3fql 3fqm 3fqq 3kn2 3kqh 3kqk 3kql 3kqn 3kqu 3q0z 3qgd 3qge 3qgf 3qgg 4nld 4u01 5e4f 5pzk 5pzl 5pzn 5pzo 5pzp 5trh 5tri 5trj 5trk 5twn

(-) Related Entries Specified in the PDB File

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