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(-) Description

Title :  CRYSTAL STRUCTURE OF CODAKINE AT 1.3A RESOLUTION
 
Authors :  J. P. Gourdine, G. C. Cioci, L. Miguet, C. Unverzagt, A. Varrot, C. Gauthier, E. J. Smith-Ravin, A. Imberty
Date :  30 May 08  (Deposition) - 05 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Sugar-Binding Protein, C-Type, Lectin, Mannose, Codakine, Invertebrate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Gourdine, G. C. Cioci, L. Miguet, C. Unverzagt, D. V. Silva, A. Varrot, C. Gautier, E. J. Smith-Ravin, A. Imberty
High Affinity Interaction Between A Bivalve C-Type Lectin And A Biantennary Complex-Type N-Glycan Revealed By Crystallography And Microcalorimetry.
J. Biol. Chem. V. 283 30112 2008
PubMed-ID: 18687680  |  Reference-DOI: 10.1074/JBC.M804353200

(-) Compounds

Molecule 1 - CODAKINE
    Chains: A
    Fragment: RESIDUES 20-148
    Organism Scientific: CODAKIA ORBICULARIS
    Organism Taxid: 13016

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CIT1Ligand/IonCITRIC ACID
3GOL2Ligand/IonGLYCEROL
4HYP1Mod. Amino Acid4-HYDROXYPROLINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:93 , ASN A:95 , GLU A:101 , ASN A:112 , ASP A:113 , GOL A:300BINDING SITE FOR RESIDUE CA A 200
2AC2SOFTWAREGLU A:93 , ASN A:95 , GLU A:101 , ASN A:112 , ASP A:113 , CA A:200 , HOH A:2169BINDING SITE FOR RESIDUE GOL A 300
3AC3SOFTWARELYS A:20 , ASN A:56 , GLY A:57 , ASP A:58 , HOH A:2033 , HOH A:2152 , HOH A:2170BINDING SITE FOR RESIDUE GOL A 400
4AC4SOFTWAREASN A:100 , ASP A:102 , ARG A:115 , CYS A:116 , HIS A:117 , HOH A:2102 , HOH A:2148 , HOH A:2171 , HOH A:2172 , HOH A:2173 , HOH A:2174BINDING SITE FOR RESIDUE CIT A 500

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:2 -A:13
2A:30 -A:124
3A:44 -A:44
4A:103 -A:116

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:93 -Pro A:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VUV)

(-) 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:129
 aligned with Q3KVL7_9BIVA | Q3KVL7 from UniProtKB/TrEMBL  Length:148

    Alignment length:129
                                    29        39        49        59        69        79        89        99       109       119       129       139         
         Q3KVL7_9BIVA    20 GCPDGWTQFLDLCYIYQSAKASWASAQSSCQALGGILAEPDTACENEVLIHMCRENGDAGSFGPWLGGQKVGGAWQWSSSGAAFDYLRWGPNEPNNSGGNEDCLHYNWLSWNDLRCHYQASYLCQRAAE 148
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------Lectin_C-2vuvA01 A:19-126                                                                                   --- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhhhhh........eeeeeee..eeee.........................eeeee..eeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vuv A   1 GCPDGWTQFLDLCYIYQSAKASWASAQSSCQALGGILAEPDTACENEVLIHMCKENGDAGSFGPWLGGQKVGGAWQWSSSGAAFDYLRWGpNEPNNSGGNEDCLHYNWLSWNDLRCHYQASYLCQRAAE 129
                                    10        20        30        40        50        60        70        80        90|      100       110       120         
                                                                                                                     91-HYP
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2VUV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: C_Lectin (98)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q3KVL7_9BIVA | Q3KVL7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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    Glu A:93 - Pro A:94   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q3KVL7_9BIVA | Q3KVL7: 2vuz

(-) Related Entries Specified in the PDB File

2vuz CRYSTAL STRUCTURE OF CODAKINE IN COMPLEX WITH BIANTENNARY NONASACCHARIDE AT 1.7A RESOLUTION