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

(-) Description

Title :  CANAVALIN FROM JACK BEAN
 
Authors :  T. -P. Ko, J. Day, A. Macpherson
Date :  20 Nov 98  (Deposition) - 25 Nov 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Vicilin, 7S Seed Protein, Domain Duplication, Swiss Roll, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. P. Ko, J. Day, A. Mcpherson
The Refined Structure Of Canavalin From Jack Bean In Two Crystal Forms At 2. 1 And 2. 0 A Resolution.
Acta Crystallogr. , Sect. D V. 56 411 2000
PubMed-ID: 10739914  |  Reference-DOI: 10.1107/S0907444900002237
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CANAVALIN)
    Cellular Location: PROTEIN BODY
    Chains: A
    Organ: SEED
    Organism Common: JACK BEAN
    Organism Scientific: CANAVALIA ENSIFORMIS
    Organism Taxid: 3823
    Other Details: TREATED WITH LIMITED DIGESTION BY TRYPSIN
    Synonym: JACK BEAN VICILIN
    Tissue: COTYLEDON

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2CAV)

(-) Sites  (0, 0)

(no "Site" information available for 2CAV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CAV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CAV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CAV)

(-) 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:346
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:377
                                    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       385       395       405       415       
           CANA_CANEN    46 NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMPKDQIQEISKHAQSSSRKTLSSQDKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGLEQQQQQGLESMQLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDGQ 422
               SCOP domains d2cava1 A:46-225 Seed storage 7S protein                                                                                                                                                                d2cava2 A:246-422 Seed storage 7S protein                                                                                                                                         SCOP domains
               CATH domains 2cavA02 A:46-225 Jelly Rolls                                                                                                                                                                            2cavA01 A:246-422 Jelly Rolls                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeeeeeeeeeeeeeee........hhhhheeeeeeeeee.eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.eeeeeee.eeeeeeeee....eeeeeeeeee.......eeeee.......hhhhhhhhhhhhhhhh.hhhhhhhhhhh.....eeeee...--------------------..eeee.....eeeeeeeeeeeee...hhhhhhheeeeeeeeee.eeeeeeeeee.eeeeeeeeeeeeeeeeeee-----------.eeeeeeeee.eeeeeee.eeeeeeeee.eeeeeeeeee....eeeee.....hhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cav A  46 NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMPKD--------------------DKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGL-----------QLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDGQ 422
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225         -         -|      255       265       275       285       295       305       315    |    -      |335       345       355       365       375       385       395       405       415       
                                                                                                                                                                                                             225                  246                                                                       320         332
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (CANA_CANEN | P50477)
molecular function
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.

 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 2cav)
 
  Sites
(no "Sites" information available for 2cav)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cav)
 
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
  2cav
    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
  CANA_CANEN | P50477
    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
  CANA_CANEN | P50477
    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
        CANA_CANEN | P50477: 1cau 1cav 1caw 1cax 1dgr 1dgw 2cau

(-) Related Entries Specified in the PDB File

2cau CRYSTALLIZED IN CUBIC SPACEGROUP