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 :  CRYSTAL STRUCTURE OF BOMBYX MORI DENSOVIRUS 1 CAPSID
 
Authors :  B. Kaufmann, M. G. Rossmann
Date :  29 Sep 10  (Deposition) - 16 Mar 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (60x)
Keywords :  Icosahedral Virus Capsid, Virus-Like Particle, Capsid Protein, Beta- Barrel, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Kaufmann, M. El-Far, P. Plevka, V. D. Bowman, Y. Li, P. Tijssen, M. G. Rossmann
Structure Of Bombyx Mori Densovirus 1, A Silkworm Pathogen.
J. Virol. V. 85 4691 2011
PubMed-ID: 21367906  |  Reference-DOI: 10.1128/JVI.02688-10

(-) Compounds

Molecule 1 - CAPSID PROTEIN VP
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Strain: HIGH-FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: VP3 CAPSID PROTEIN RESIDUES 179-672
    Organism Scientific: BOMBYX MORI DENSOVIRUS 1
    Organism Taxid: 46253

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (60x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3P0S)

(-) Sites  (0, 0)

(no "Site" information available for 3P0S)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P0S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P0S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P0S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P0S)

(-) Exons   (0, 0)

(no "Exon" information available for 3P0S)

(-) 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:412
 aligned with Q8V0M6_BMDNV | Q8V0M6 from UniProtKB/TrEMBL  Length:672

    Alignment length:412
                                   230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630  
         Q8V0M6_BMDNV   221 ANDGRQDIFSGAPQPNQHHTLVYGKSYHFTITNGLPEFRHLATTNSGYYAQQRFKHIHGIPWERLLMYVSEGELLRMFRDYTSLKVEEVVCEVYSLGVRLPFVTSATTSSVANANAQYPIGCFHFDEAYETNYGINNVADIINKALGTEWKNATRPTAAVTTAWSEQFPNISASSTSRDINNPVIVDYSLPYFENNVPKDVGIYDYVDIKNGTTAYGKCWEKRFKPTNGLLYAESTLKGNVVTPLAAQPTNIMTPIPGLENGYFMSNDQIRERRDLTTSVPPVALTATKLNQSASNNLNAFVDYMGYNYFGEQKCAPQSMPKFMIGFVNIRNEDNSLLNAKWDILIKTRIRLTGLQSTREWVARTDRIPPQYFTSQYTQFRYPNINETPLLRSLGTFKLPTKRPGMDSRIAA 632
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Parvo_NS1-3p0sA01 A:43-227                                                                                                                                                               ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeeeeeeeeee...eeeeeeee...eeeeeeeeeeeeee...hhhhh.hhhhhhhhh....eeeeeeeeeeeeeeeee...................eeeee.hhhh.eee.hhhhhhhhhhhhhh..............................ee...eeeeeee............hhhh.eeeee.....eeeeeeee.....eeee.............................eeee..eeee.hhh......eeee......hhhhhhh.......ee..............eeeee.............eeeeeeeeeeeeeeee.....................eeee.........ee.....ee...ee.ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p0s A  43 ANDGRQDIFSGAPQPNQHHTLVYGKSYHFTITNGLPEFRHLATTNSGYYAQQRFKHIHGIPWERLLMYVSEGELLRMFRDYTSLKVEEVVCEVYSLGVRLPFVTSATTSSVANANAQYPIGCFHFDEAYETNYGINNVADIINKALGTEWKNATRPTAAVTTAWSEQFPNISASSTSRDINNPVIVDYSLPYFENNVPKDVGIYDYVDIKNGTTAYGKCWEKRFKPTNGLLYAESTLKGNVVTPLAAQPTNIMTPIPGLENGYFMSNDQIRERRDLTTSVPPVALTATKLNQSASNNLNAFVDYMGYNYFGEQKCAPQSMPKFMIGFVNIRNEDNSLLNAKWDILIKTRIRLTGLQSTREWVARTDRIPPQYFTSQYTQFRYPNINETPLLRSLGTFKLPTKRPGMDSRIAA 454
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452
   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 3P0S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P0S)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8V0M6_BMDNV | Q8V0M6)
biological process
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.

 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 3p0s)
 
  Sites
(no "Sites" information available for 3p0s)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3p0s)
 
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
  3p0s
    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
  Q8V0M6_BMDNV | Q8V0M6
    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
  Q8V0M6_BMDNV | Q8V0M6
    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 3P0S)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3P0S)