Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  APO CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH BETA HAIRPIN LOOP DELETION
 
Authors :  T. E. Edwards, R. T. Mosley
Date :  16 Mar 12  (Deposition) - 18 Apr 12  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Rdrp, Loopless Delta8, Flaviviridae, Hepatitis C Virus, Viral Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. T. Mosley, T. E. Edwards, E. Murakami, A. M. Lam, R. L. Grice, J. Du, M. J. Sofia, P. A. Furman, M. J. Otto
Structure Of Hepatitis C Virus Polymerase In Complex With Primer-Template Rna.
J. Virol. V. 86 6503 2012
PubMed-ID: 22496223  |  Reference-DOI: 10.1128/JVI.00386-12

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: VCID 5854
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SEE REMARK 999
    Gene: NS5B
    Mutation: YES
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS
    Organism Taxid: 356411
    Strain: JFH-1
    Synonym: NS5B, P68

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SO47Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:48 , LYS A:155 , ARG A:222BINDING SITE FOR RESIDUE SO4 A 601
2AC2SOFTWAREPRO A:93 , SER A:96 , ARG A:168 , LYS A:172 , HOH A:797 , HOH A:863BINDING SITE FOR RESIDUE SO4 A 602
3AC3SOFTWAREGLY A:375 , PRO A:376 , ARG A:377 , GLY A:378 , ARG A:379 , ARG A:381BINDING SITE FOR RESIDUE SO4 A 603
4AC4SOFTWAREARG A:422 , SER A:473 , MET A:474 , HIS A:475 , ASN A:527 , TRP A:528 , LYS A:533 , HOH A:849BINDING SITE FOR RESIDUE SO4 A 604
5AC5SOFTWAREARG A:505 , VAL A:530 , LYS A:531 , THR A:532 , HOH A:861BINDING SITE FOR RESIDUE SO4 A 605
6AC6SOFTWARESER A:510 , ARG A:514BINDING SITE FOR RESIDUE SO4 A 606
7AC7SOFTWAREPRO A:94 , GLY A:104 , ALA A:105 , LYS A:106 , GLU A:107 , HOH A:771BINDING SITE FOR RESIDUE SO4 A 607
8AC8SOFTWAREPHE A:145 , ARG A:386 , THR A:390BINDING SITE FOR RESIDUE EDO A 608

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E76)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E76)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E76)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E76)

(-) Exons   (0, 0)

(no "Exon" information available for 4E76)

(-) 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:544
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4e76a_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.eee..........................hhh.eee.hhhhhhhhhhhhh.ee....hhhhhhhhhhhhhhhhh......hhhhhhhh............hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeee...eee............eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh.....eeeeee.....eeeeee..hhhhhhhhh.......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e76 A   0 SSMSYSWTGALITPCSPEEEKLPINPLSNSLLRYHNKVYCTTSKSASQRAKKVTFDRTQVLDAHYDSVLKDIKLAASKVSARLLTLQQACQLTPPHSARSKYGFGAKEVRSLSGRAVNHIKSVWKDLLEDPQTPIPTTIMAKNEVFCVDPAKGGKKPARLIVYPDLGVRVCEKMALYDITQKLPQAVMGASYGFQYSPAQRVEYLLKAWAEKKDPMGFSYDTRCFDSTVTERDIRTEESIYQACSLPEEARTAIHSLTERLYVGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCYVKALAACKAAGIVAPTMLVCGDDLVVISESQGTEEDERNLRAFTEAMTRYSAPPGDPPRPEYDLELITSCSSNVSVALGPRGRRRYYLTRDPTTPLARAAWETVRHSPINSWLGNIIQYAPTIWVRMVLMTHFFSILMVQDTLDQNLGGVNPLDLPAIIERLHGLDAFSMHTYSHHELTRVASALRKLGAPPLRVWKSRARAVRASLISRGGKAAVCGRYLFNWAVKTKLKLTPLPEARLLDLSSWF 551
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439     ||457       467       477       487       497       507       517       527       537       547    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       445|                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        454
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E76)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E76)

(-) Gene Ontology  (92, 92)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4e76)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4e76
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  POLG_HCVJF | Q99IB8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.48
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  POLG_HCVJF | Q99IB8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4e78 NS5B BOUND TO PRIMER-TEMPLATE WITH 3'-DG
4e7a NS5B BOUND TO PRIMER-TEMPLATE WITH 2',3'-DDC