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

(-) Description

Title :  HIBISCUS LATENT SINGAPORE VIRUS
 
Authors :  S. K. Tewary, S. M. Wong, K. Swaminathan
Date :  22 Oct 10  (Deposition) - 12 Jan 11  (Release) - 19 Jan 11  (Revision)
Method :  FIBER DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  P,R
Biol. Unit 1:  P,R  (49x)
Keywords :  Helical Virus, Virus-Rna Complex, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Tewary, T. Oda, A. Kendall, W. Bian, G. Stubbs, S. M. Wong, K. Swaminathan
Structure Of Hibiscus Latent Singapore Virus By Fiber Diffraction: A Non-Conserved His122 Contributes To Coat Protein Stability
J. Mol. Biol. 2010
PubMed-ID: 21195089  |  Reference-DOI: 10.1016/J.JMB.2010.12.032

(-) Compounds

Molecule 1 - RNA (5'-R(P*GP*AP*A)-3')
    Chains: R
    Engineered: YES
    Other Details: SYNTHETIC RNA
    Synthetic: YES
 
Molecule 2 - COAT PROTEIN
    Chains: P
    Organism Scientific: HIBISCUS LATENT SINGAPORE VIRUS
    Organism Taxid: 185955

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : PR
Biological Unit 1 (49x): PR

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3PDM)

(-) Sites  (0, 0)

(no "Site" information available for 3PDM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PDM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PDM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PDM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PDM)

(-) Exons   (0, 0)

(no "Exon" information available for 3PDM)

(-) 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 P from PDB  Type:PROTEIN  Length:162
 aligned with Q8BE68_9VIRU | Q8BE68 from UniProtKB/TrEMBL  Length:163

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
         Q8BE68_9VIRU     2 PYLNLTPLNLIYTSGTFAPYDVFLEILVKSRSNSFQTQAGRDTLREQLINSLQIVANLNTRYPLLGFYVWVRNPTLAPVFEALLRATDTKNRIIEVEEESRPTTAETLNATQRVDDATVAIHKEIDNILLLLQGGTAVYDRTAFEVVSGLSWADPTTTSTTT 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains TMV_coat-3pdmP01 P:1-145                                                                                                                         ----------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhh.........hhhhhhhhhhhh.........................hhhhhhhhhh................hhhhh....hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pdm P   1 PYLNLTPLNLIYTSGTFAPYDVFLEILVKSRSNSFQTQAGRDTLREQLINSLQIVANLNTRYPLLGFYVWVRNPTLAPVFEALLRATDTKNRIIEVEEESRPTTAETLNATQRVDDATVAIHKEIDNILLLLQGGTAVYDRTAFEVASGLSWADPTTTSTTT 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain R from PDB  Type:RNA  Length:3
                                   
                 3pdm R   1 GAA   3
   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 3PDM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PDM)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: TMV_coat] (6)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain P   (Q8BE68_9VIRU | Q8BE68)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

 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
(no "Ligands, Modified Residues, Ions" information available for 3pdm)
 
  Sites
(no "Sites" information available for 3pdm)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pdm)
 
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 | Biol. Unit 1 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
  3pdm
    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
  Q8BE68_9VIRU | Q8BE68
    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
  Q8BE68_9VIRU | Q8BE68
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3PDM)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3PDM)