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 :  2.10
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 LocationPROTEIN BODY
    ChainsA
    OrganSEED
    Organism CommonJACK BEAN
    Organism ScientificCANAVALIA ENSIFORMIS
    Organism Taxid3823
    Other DetailsTREATED WITH LIMITED DIGESTION BY TRYPSIN
    SynonymJACK BEAN VICILIN
    TissueCOTYLEDON

 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 2CAU)

(-) Sites  (0, 0)

(no "Site" information available for 2CAU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CAU)

(-) 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:344
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:376
                                    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 NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMPKDQIQEISKHAQSSSRKTLSSQDKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGLEQQQQQGLESMQLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDG 421
               SCOP domains d2caua1 A:46-223 Seed storage 7S protein                                                                                                                                                                d2caua2 A:246-421 Seed storage 7S protein                                                                                                                                        SCOP domains
               CATH domains 2cauA02 A:46-223 Jelly Rolls                                                                                                                                                                            2cauA01 A:246-419 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
                 2cau A  46 NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMP----------------------DKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGLE----------QLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDG 421
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       | -         -         -|      255       265       275       285       295       305       315     |   -      |335       345       355       365       375       385       395       405       415      
                                                                                                                                                                                                           223                    246                                                                        321        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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 2cau)
 
  Sites
(no "Sites" information available for 2cau)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cau)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2cau
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CANA_CANEN | P50477
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CANA_CANEN | P50477
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CANA_CANEN | P504771cau 1cav 1caw 1cax 1dgr 1dgw 2cav

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2CAU)