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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA- DEPENDENT RNA POLYMERASE IN COMPLEX WITH 5-[3-(TERT-BUTYLCARBAMOYL)PHENYL]-6-(ETHYLAMINO)-2-(4-FLUOROPHENYL)-N-METHYLFURO[2,3-B]PYRIDINE-3-CARBOXAMIDE
 
Authors :  S. Sheriff
Date :  14 Nov 16  (Deposition) - 15 Mar 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.04
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ns5B, Polymerase, Hcv, Fingers, Palm, Thumb, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Eastman, K. Parcella, K. -S. Yeung, K. Grant-Young, J. Zhu, T. Wang, Z. Zhang, Z. Yin, B. R. Beno, S. Sheriff, K. Kish, J. Tredup, A. G. Jardel, N. Szapiel, V. Halan, K. Ghosh, D. Parker, K. Mosure, H. Fang, Y. -K. Wang, J. Lemm, X. Zhuo, U. Hanumegowda, M. Liu, K. Rigat, M. Donoso, M. Tuttle, T. Zvyaga, Z. Haarhoff, N. A. Meanwell, M. Soars, S. B. Roberts, J. F. Kadow
The Discovery Of A Pan-Genotypic, Primer Grip Inhibitor Of Hcv Ns5B Polymerase
Medchemcomm V. 8 796 2017
PubMed: search  |  Reference-DOI: 10.1039/C6MD00636A

(-) 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: PET21B
    Expression System Strain: BL21(DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2420-2992
    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  (3, 15)

Asymmetric Unit (3, 15)
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
27NG1Ligand/Ion5-[3-(TERT-BUTYLCARBAMOYL)PHENYL]-6-(ETHYLAMINO)-2-(4-FLUOROPHENYL)-N-METHYLFURO[2,3-B]PYRIDINE-3-CARBOXAMIDE
3SO412Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
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
27NG-1Ligand/Ion5-[3-(TERT-BUTYLCARBAMOYL)PHENYL]-6-(ETHYLAMINO)-2-(4-FLUOROPHENYL)-N-METHYLFURO[2,3-B]PYRIDINE-3-CARBOXAMIDE
3SO46Ligand/IonSULFATE ION
Biological Unit 2 (3, 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
27NG1Ligand/Ion5-[3-(TERT-BUTYLCARBAMOYL)PHENYL]-6-(ETHYLAMINO)-2-(4-FLUOROPHENYL)-N-METHYLFURO[2,3-B]PYRIDINE-3-CARBOXAMIDE
3SO46Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:395 , ALA A:396 , LEU A:492 , GLY A:493 , VAL A:494 , PRO A:495 , PRO A:496 , ARG A:498 , VAL A:499 , ARG A:503 , 23E B:601binding site for residue 23E A 601
02AC2SOFTWARESER A:84 , VAL A:85 , ARG A:120binding site for residue SO4 A 602
03AC3SOFTWAREARG A:48 , LYS A:51 , ARG A:158 , THR A:221 , CYS A:223binding site for residue SO4 A 603
04AC4SOFTWAREHIS A:374 , SER A:476 , ARG A:517 , MET A:573binding site for residue SO4 A 604
05AC5SOFTWAREPRO A:496 , LEU A:497 , ARG A:498 , ARG A:570binding site for residue SO4 A 605
06AC6SOFTWAREGLU A:361 , SER A:371 , SER A:478binding site for residue SO4 A 606
07AC7SOFTWARELYS A:79 , ASP A:244 , LEU B:60 , LEU B:68binding site for residue SO4 A 607
08AC8SOFTWARETHR A:399 , ALA A:400 , HIS A:428 , 23E A:601 , LEU B:392 , ALA B:395 , ALA B:396 , ILE B:424 , HIS B:428 , LEU B:492 , GLY B:493 , VAL B:494 , PRO B:495 , PRO B:496 , ARG B:498 , VAL B:499 , ARG B:503binding site for residue 23E B 601
09AC9SOFTWAREARG 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:415 , TYR B:452 , PHE B:551binding site for residue 7NG B 602
10AD1SOFTWARESER B:84 , VAL B:85 , GLU B:86 , ARG B:120binding site for residue SO4 B 603
11AD2SOFTWAREGLY B:516 , ARG B:517binding site for residue SO4 B 604
12AD3SOFTWARESER A:1 , LYS B:379 , ARG B:380binding site for residue SO4 B 605
13AD4SOFTWAREHIS B:475 , SER B:476binding site for residue SO4 B 606
14AD5SOFTWAREARG B:48 , LYS B:51 , CYS B:223binding site for residue SO4 B 607
15AD6SOFTWAREMET B:187 , GLY B:188 , SER B:189binding site for residue SO4 B 608

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:449 -Ala B:450

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TWN)

(-) 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:550
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..............hhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee..................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh.................ee..eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhh.ee..............eee.ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5twn A   1 SMSYTWTGALITPCYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSLSRARPRWFM 573
                                    10   ||   43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573
                                        14|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                         38                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:536
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..............hhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeeee...........eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhh.ee..eeeeeee.....eeeeee..hhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeee....eeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh............hhhhh...hhhhhh.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5twn B   1 SMSYTWTGALITPCYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSARSKFGYGAKDVRNLSSKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPGQRVEFLVNAWKAKKCPMGFAYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKAAAACRAAKLQDCTMLVCGDDLVVICESAGTQEDEASLRAFTEAMTRYSAPPGDPPKPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIQRLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVRTKLKLTPIPAASQLDLSSWFVAGYSGGDIYHSL 564
                                    10   ||   43        53        63        73        83        93       103       113       123       133       143     ||158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558      
                                        14|                                                                                                            149|                                                                                                                                                                                                                                                                                                                                                                                                                         
                                         38                                                                                                             155
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 74)

Asymmetric Unit(hide GO term definitions)

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  5twn
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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 5pzm 5pzn 5pzo 5pzp 5trh 5tri 5trj 5trk

(-) Related Entries Specified in the PDB File

5twm