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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 L30S 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 :  1.97
Chains :  Asym./Biol. Unit :  A
Keywords :  Rdrp Structure (Fingers, Palm, Thumb Domains), Acetylation, Apoptosis, Atp-Binding, Capsid Protein, Cell Membrane, Cytoplasm, Disulfide Bond, Endoplasmic Reticulum, Envelope Protein, Fusion Protein, Glycoprotein, Helicase, Host-Virus Interaction, Hydrolase, Interferon Antiviral System Evasion, Lipid Droplet, Lipoprotein, Membrane, Metal-Binding, Mitochondrion, Multifunctional Enzyme, Nucleotide-Binding, Nucleotidyltransferase, Nucleus, Oncogene, Palmitate, Phosphoprotein, Protease, Ribonucleoprotein, Rna Replication, Rna-Binding, Rna-Directed Rna Polymerase, Secreted, Serine Protease, Sh3-Binding, Thiol Protease, Transcription, Transcription Regulation, Transferase, Transmembrane, Ubl Conjugation, Viral Nucleoprotein, Virion, Zinc, 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
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: ROSETTA 2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2443-3015
    Gene: NS5B
    Mutation: YES
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS GENOTYPE 2A (ISOLATE JFH-1)
    Organism Taxid: 356411
    Strain: ISOLATE JFH-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
17NG1Ligand/Ion5-[3-(TERT-BUTYLCARBAMOYL)PHENYL]-6-(ETHYLAMINO)-2-(4-FLUOROPHENYL)-N-METHYLFURO[2,3-B]PYRIDINE-3-CARBOXAMIDE
2PE51Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
3PG42Ligand/IonTETRAETHYLENE GLYCOL
4SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:200 , LEU A:204 , LEU A:314 , ASP A:319 , VAL A:321 , ILE A:363 , SER A:365 , CYS A:366 , SER A:368 , LEU A:384 , GLN A:414 , TYR A:415 , TYR A:448 , PHE A:551 , HOH A:767binding site for residue 7NG A 601
2AC2SOFTWAREASN A:24 , SER A:27 , HOH A:912binding site for residue SO4 A 602
3AC3SOFTWAREGLU A:446 , GLY A:449 , GLY A:556 , GLY A:557 , GLY A:558 , HOH A:777binding site for residue SO4 A 603
4AC4SOFTWAREGLU A:361 , SER A:371 , VAL A:372 , SER A:478 , HOH A:756 , HOH A:765binding site for residue SO4 A 604
5AC5SOFTWAREARG A:48 , ARG A:158 , ARG A:222 , CYS A:223binding site for residue SO4 A 605
6AC6SOFTWARELYS A:100 , TYR A:101 , PRO A:135 , THR A:137 , PHE A:267 , ASN A:268 , SER A:269 , GLY A:271 , HOH A:808binding site for residue PE5 A 606
7AC7SOFTWAREGLU A:143 , PHE A:145 , CYS A:146 , SER A:367 , ARG A:386 , THR A:390 , ARG A:394binding site for residue PG4 A 607
8AC8SOFTWARETRP A:6 , GLY A:8 , ALA A:9 , SER A:46 , ALA A:49 , ALA A:209 , GLU A:210 , LYS A:211 , HOH A:927binding site for residue PG4 A 608

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:557 -Gly A:558

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TWM)

(-) Sequences/Alignments

Asymmetric/Biological 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....................hhhhhhhhhheee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee...eee........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhh.hhhhh........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5twm A   1 SMSYSWTGALITPCSPEEEKLPINPLSNSSLRYHNKVYCTTSKSASQRAKKVTFDRTQVLDAHYDSVLKDIKLAASKVSARLLTLEEACQLTPPHSARSKYGFGAKEVRSLSGRAVNHIKSVWKDLLEDPQTPIPTTIMAKNEVFCVDGKKPARLIVYPDLGVRVCEKMALYDITQKLPQAVMGASYGFQYSPAQRVEYLLKAWAEKKDPMGFSYDTRCFDSTVTERDIRTEESIYQACSLPEEARTAIHSLTERLYVGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCYVKALAACKAAGIVAPTMLVCGDDLVVISESQGTEEDERNLRAFTEAMTRYSAPPGDPPRPEYDLELITSCSSNVSVALGPRGRRRYYLTRDPTTPLARAAWETVRHSPINSWLGNIIQYAPTIWVRMVLMTHFFSILMVQDTLDQNLNFEMYGSVYSVNPLDLPAIIERLHGLDAFSMHTYSHHELTRVASALRKLGAPPLRVWKSRARAVRASLISRGGKAAVCGRYLFNWAVKTKLKLTPLPEARLLDLSSWFTVGAGGGDIFHS 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         
                                                                                                                                                                             148|                                                                                                                                                                                                                                                                                                                                                                                                                          
                                                                                                                                                                              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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (92, 92)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:557 - Gly A:558   [ RasMol ]  
 

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UniProtKB/Swiss-Prot
        POLG_HCVJF | Q99IB8: 2kzq 2lif 2lvg 2xxd 2xym 3i5k 4aep 4aex 4e76 4e78 4e7a 4j1v 4obc 4wt9 4wta 4wtc 4wtd 4wte 4wtf 4wtg 4wti 4wtj 4wtk 4wtl 4wtm 5uj2

(-) Related Entries Specified in the PDB File

5twn