Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY AND PROTEASE INHIBITION IN NORWALK VIRUS
 
Authors :  B. V. V. Prasad, Z. Muhaxhiri, L. Deng, S. Shanker, B. Sankaran, M. K. Est T. Palzkill, Y. Song
Date :  03 Jan 13  (Deposition) - 20 Feb 13  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Muhaxhiri, L. Deng, S. Shanker, B. Sankaran, M. K. Estes, T. Palzkill, Y. Song, B. V. Prasad
Structural Basis Of Substrate Specificity And Protease Inhibition In Norwalk Virus.
J. Virol. V. 87 4281 2013
PubMed-ID: 23365454  |  Reference-DOI: 10.1128/JVI.02869-12

(-) Compounds

Molecule 1 - GENOME POLYPROTEIN
    Chains: A
    EC Number: 3.6.1.15, 3.4.22.66, 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: NORWALK VIRUS PROTEASE (UNP RESIDUES 1101-1281)
    Gene: ORF1
    Organism Common: HU/NV/NV/1968/US
    Organism Scientific: NOROVIRUS HU/1968/US
    Organism Taxid: 524364
    Strain: GI/HUMAN/UNITED STATES/NORWALK/1968
    Synonym: PROTEIN P48, NTPASE, P41, PROTEIN P22, VIRAL GENOME-LINKED PROTEIN, VPG, 3C-LIKE PROTEASE, 3CLPRO, CALICIVIRIN, RNA-DIRECTED RNA POLYMERASE, RDRP
 
Molecule 2 - PEPTIDE INHIBITOR, SYC 10
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
11HB1Mod. Amino Acid(4S)-4-AMINO-5-HYDROXY-N,N-DIMETHYLPENTANAMIDE
2NA1Ligand/IonSODIUM ION
3PHQ1Mod. Amino AcidBENZYL CHLOROCARBONATE
4SCN4Ligand/IonTHIOCYANATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
11HB2Mod. Amino Acid(4S)-4-AMINO-5-HYDROXY-N,N-DIMETHYLPENTANAMIDE
2NA-1Ligand/IonSODIUM ION
3PHQ2Mod. Amino AcidBENZYL CHLOROCARBONATE
4SCN8Ligand/IonTHIOCYANATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:2 , THR A:4 , LEU A:5 , ARG A:8BINDING SITE FOR RESIDUE SCN A 201
2AC2SOFTWARELYS A:0BINDING SITE FOR RESIDUE NA A 202
3AC3SOFTWAREVAL A:82 , SER A:84 , HIS A:145 , LYS A:146 , HOH A:344 , HOH A:366 , HOH A:389BINDING SITE FOR RESIDUE SCN A 203
4AC4SOFTWAREHIS A:50 , GLN A:172 , ALA A:173BINDING SITE FOR RESIDUE SCN A 204
5AC5SOFTWARELYS A:37 , HOH A:369 , HOH A:403BINDING SITE FOR RESIDUE SCN A 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IMZ)

(-) 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:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhheeee..eeeee....eeeee.hhh.....ee..ee...eeeeee..eeeeee...........ee........eeeeeee.....eeeeeeeeeeeeeeee..eeeeeeeeee....hhhhh..eeeeee..eeeeeeeeeee.....eeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imz A  -1 DKAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRIQGRLVHGQSGMLLTGTIPGDCGAPYVHKRGNDWVVCGVHAAATKSGNTVVCAVQAGEGETAE 181
                                     8        18        28        38        48        58        68        78        88        98       108       118    || 137       147       157       167       177 ||
                                                                                                                                                      123|                                           179|
                                                                                                                                                       133                                            181


Chain B from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4imz B   1 xLFx   4
                            |  |
                            |  |
                            1-PHQ
                               4-1HB
   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 4IMZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    1HB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PHQ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SCN  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4imz)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4imz
    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_NVN68 | Q83883
    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
  3.4.22.66
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.6.1.15
    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_NVN68 | Q83883
    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_NVN68 | Q83883: 2fyq 2fyr 2lnc 3ur6 3ur9 4imq 4in1 4in2 4inh 4xbb 4xbc 4xbd 5dg6 5dgj 5e0g 5e0h 5e0j 5t6d 5t6f 5t6g 5tg1 5tg2

(-) Related Entries Specified in the PDB File

4imq 4in2 4inh 4iro