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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE MURINE NOROVIRUS NS6 PROTEASE (INACTIVE C139A MUTANT) WITH A C-TERMINAL EXTENSION TO INCLUDE RESIDUES P1 PRIME - P4 PRIME OF NS7
 
Authors :  E. N. Leen, H. Cromwell Jr, H. Fernandes, S. Curry
Date :  27 Nov 14  (Deposition) - 18 Feb 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.47
Chains :  Asym./Biol. Unit :  A
Keywords :  Murine Norovirus Protease, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Fernandes, E. N. Leen, H. Cromwell, M. P. Pfeil, S. Curry
Structure Determination Of Murine Norovirus Ns6 Proteases With C-Terminal Extensions Designed To Probe Protease-Substrate Interactions.
Peerj V. 3 E798 2015
PubMed-ID: 25755927  |  Reference-DOI: 10.7717/PEERJ.798
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NS6 PROTEASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Fragment: UNP RESIDUES 998-1173
    Mutation: YES
    Organism Scientific: MURINE NOROVIRUS 1
    Organism Taxid: 223997

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4X2X)

(-) Sites  (0, 0)

(no "Site" information available for 4X2X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X2X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X2X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X2X)

(-) Exons   (0, 0)

(no "Exon" information available for 4X2X)

(-) 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:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeee..eeeee....eeeee.hhh..............eeeeee..eeeeee...........ee........eeeeeee.....eeeeeeeeeeeeeeee..eeeeeeeeee.....hhhhh..eeeeee..eeeeeeeeeee...eeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x2x A   4 SIWSRVVQFGTGWGFWVSGHVFITAKHVAPPKGTEIFGRKPGDFTVTSSGDFLKYYFTSAVRPDIPAMVLENGCQEGVVASVLVKRASGEMLALAVRMGSQAAIKIGSAVVHGQTGMLLTGGTIPGDAGCPYVYKKGNTWVVIGVHVAATGNTVIAATHGEPTLEA 179
                                    13        23        33        43        53        63        73        83        93       103       113       123||     141       151       161|      173      
                                                                                                                                                  124|                         161|               
                                                                                                                                                   133                          164
   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  (0, 0)

(no "SCOP Domain" information available for 4X2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X2X)

(-) Gene Ontology  (18, 18)

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
(no "Ligands, Modified Residues, Ions" information available for 4x2x)
 
  Sites
(no "Sites" information available for 4x2x)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4x2x)
 

(-) 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 ](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
  4x2x
    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
  Q80J95_9CALI | Q80J95
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q80J95_9CALI | Q80J95
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q80J95_9CALI | Q80J95: 2m4g 2mcd 2mch 3nah 3nai 3qid 3sfg 3sfu 3upf 3uqs 3ur0 4ash 4nru 4o4r 4x2v 4x2w 4x2y

(-) Related Entries Specified in the PDB File

4ash THIS ENTRY CONTAINS C TERMINAL EXTENSION TO INCLUDE RESIDUE P1 PRIME TO P4 PRIME OF NS7 IN ADDITION TO 4ASH
4x2v
4x2w