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 :  THE BACTERIOPHAGE PRD1 COAT PROTEIN, P3, IS STRUCTURALLY SIMILAR TO HUMAN ADENOVIRUS HEXON
 
Authors :  S. D. Benson, J. K. H. Bamford, D. H. Bamford, R. M. Burnett
Date :  12 Apr 99  (Deposition) - 20 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Bacteriophage Prd1, Coat Protein, Jelly Roll, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Benson, J. K. Bamford, D. H. Bamford, R. M. Burnett
Viral Evolution Revealed By Bacteriophage Prd1 And Human Adenovirus Coat Protein Structures.
Cell(Cambridge, Mass. ) V. 98 825 1999
PubMed-ID: 10499799  |  Reference-DOI: 10.1016/S0092-8674(00)81516-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (MAJOR CAPSID PROTEIN (P3))
    Chains: A, B, C
    Engineered: YES
    Expression System: SALMONELLA TYPHIMURIUM
    Expression System Taxid: 602
    Expression System Vector: BACTERIOPHAGE PRD1
    Expression System Vector Type: VIRUS
    Organism Scientific: ENTEROBACTERIA PHAGE PRD1
    Organism Taxid: 10658

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1CJD)

(-) Sites  (0, 0)

(no "Site" information available for 1CJD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CJD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CJD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CJD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CJD)

(-) Exons   (0, 0)

(no "Exon" information available for 1CJD)

(-) 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:369
 aligned with CAPSD_BPPRD | P22535 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:369
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374         
          CAPSD_BPPRD    15 LRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSR 383
               SCOP domains d1cjda1 A:15-244 Coat protein p3                                                                                                                                                                                                      d1cjda2 A:245-383 Coat protein p3                                                                                                           SCOP domains
               CATH domains 1cjdA01 A:15-243 Viral coat protein p3                                                                                                                                                                                               1cjdA02 A:244-383  [code=2.60.120.20, no name defined]                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.eeeeeeeeeeee......eeee......eeeeeeeeeeeeeee............hhhh.eeeeeee........eeehhhhhhhhhhhh.................................eeeeeeeeeee.....................eeeeee.......................hhheee.eeeeeeeeeeee............hhhhheeeeeeeeee.......eeeee.....eeeeeeeeeee.........eeeeeeee..........hhhhhhhhhhhh.......eeeee.......hhhh..eeeeeee......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cjd A  15 LRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSR 383
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374         


Chain B from PDB  Type:PROTEIN  Length:372
 aligned with CAPSD_BPPRD | P22535 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:372
                                    22        32        42        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  
          CAPSD_BPPRD    13 AALRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRT 384
               SCOP domains d1cjdb1 B:13-244 Coat protein p3                                                                                                                                                                                                        d1cjdb2 B:245-384 Coat protein p3                                                                                                            SCOP domains
               CATH domains 1cjdB01 B:13-243 Viral coat protein p3                                                                                                                                                                                                 1cjdB02 B:244-384  [code=2.60.120.20, no name defined]                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee......eeee......eeeeeeeeeeeeeee............hhhh.eeeeeee........eeehhhhhhhhhhhh.................................eeeeeeeeeee.....................eeeeee.......................hhheee.eeeeeeeeeeee............hhhhheeeeeeeeeee......eeeee.....eeeeeeeeeee.........eeeeeeee..........hhhhhhhhhhhh.......eeeee.............eeeeeee......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cjd B  13 AALRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRT 384
                                    22        32        42        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  


Chain C from PDB  Type:PROTEIN  Length:367
 aligned with CAPSD_BPPRD | P22535 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:369
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375         
          CAPSD_BPPRD    16 RNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRT 384
               SCOP domains d1cjdc1 C:16-244 Coat protein p3                                                                                                                                                                                                     --d1cjdc2 C:247-384 Coat protein p3                                                                                                          SCOP domains
               CATH domains 1cjdC01 C:16-243 Viral coat protein p3                                                                                                                                                                                              1  cjdC02 C:244-384  [code=2.60.120.20, no name defined]                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.eeeeeeeeeeee......eeee......eeeeeeeeeeeeeee............hhhh.eeeeeee........eeehhhhhhhhhhhh.................................eeeeeeeeeee.....................eeeeee..hhhh.................hhheee.eeeeeeeeeeee......--......hhheeeeeeeeeee......eeeee.....eeeeeeeeeee.........eeeeeeee..........hhhhhhhhhhhh.......eeeee.......hhh...eeeeeee......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cjd C  16 RNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQ--YILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRT 384
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235        |- |     255       265       275       285       295       305       315       325       335       345       355       365       375         
                                                                                                                                                                                                                                                              244  |                                                                                                                                         
                                                                                                                                                                                                                                                                 247
   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, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CJD)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CAPSD_BPPRD | P22535)
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/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 1cjd)
 
  Sites
(no "Sites" information available for 1cjd)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1cjd)
 

(-) 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
  1cjd
    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
  CAPSD_BPPRD | P22535
    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)
  (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
  CAPSD_BPPRD | P22535
    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
        CAPSD_BPPRD | P22535: 1gw7 1gw8 1hb5 1hb7 1hb9 1hqn 1hx6 1w8x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CJD)