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 :  STRUCTURE OF NEW ANTIGEN RECEPTOR VARIABLE DOMAIN FROM SHARKS
 
Authors :  V. A. Streltsov, J. A. Carmichael, S. D. Nuttall
Date :  18 May 05  (Deposition) - 25 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Ig Vnar, Natural Type2, 12A-9, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Streltsov, J. A. Carmichael, S. D. Nuttall
Structure Of A Shark Ignar Antibody Variable Domain And Modeling Of An Early-Developmental Isotype.
Protein Sci. V. 14 2901 2005
PubMed-ID: 16199666  |  Reference-DOI: 10.1110/PS.051709505

(-) Compounds

Molecule 1 - NEW ANTIGEN RECEPTOR VARIABLE DOMAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGC
    Expression System Strain: TG1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: SPOTTED WOBBEGONG
    Organism Scientific: ORECTOLOBUS MACULATUS
    Organism Taxid: 168098

 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 2COQ)

(-) Sites  (0, 0)

(no "Site" information available for 2COQ)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:83
2A:29 -A:89

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:6 -Pro A:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2COQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2COQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2COQ)

(-) 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:108
 aligned with Q8JJ25_9CHON | Q8JJ25 from UniProtKB/TrEMBL  Length:108

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
         Q8JJ25_9CHON     1 ARVDQTPRIATKETGESLTINCVLRDTACALDSTNWYRTKLGSTKEQTISIGGRYSETVDEGSNSASLTIRDLRVEDSGTYKCKAYRRCAFNTGVGYKEGAGTVLTVK 108
               SCOP domains d2coqa_ A: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee....eeeeeeeeeeee.....eee......eeeeee....eeeeee...hhhh.eeeeeeeeeee........ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2coq A   1 ARVDQTPRIATKETGESLTINCVLRDTACALDSTNWYRTKLGSTKEQTISIGGRYSETVDEGSNSASLTIRDLRVEDSGTYKCKAYRRCAFNTGVGYKEGAGTVLTVK 108
                                    10        20        30        40        50        60        70        80        90       100
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2COQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2COQ)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2COQ)

 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 2coq)
 
  Sites
(no "Sites" information available for 2coq)
 
  Cis Peptide Bonds
    Thr A:6 - Pro A:7   [ RasMol ]  
 

(-) 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
  2coq
    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
  Q8JJ25_9CHON | Q8JJ25
    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
  Q8JJ25_9CHON | Q8JJ25
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8JJ25_9CHON | Q8JJ25: 5l8j 5l8k 5l8l

(-) Related Entries Specified in the PDB File

1ver SIMILAR PROTEIN 12Y-1
1ves SIMILAR PROTEIN 12Y-2