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(-) Description

Title :  CRYSTAL STRUCTURE OF CODAKINE IN COMPLEX WITH BIANTENNARY NONASACCHARIDE AT 1.7A RESOLUTION
 
Authors :  J. P. Gourdine, G. C. Cioci, L. Miguet, C. Unverzagt, A. Varrot, C. Gauth E. J. Smith-Ravin, A. Imberty
Date :  02 Jun 08  (Deposition) - 05 Aug 08  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Nonasaccharide, Codakia Orbicularis, Sugar-Binding Protein, C-Type, Lectin, Codakine, Biantennary, Invertebrate, Sugar Binding Protein (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  (6, 12)

Asymmetric/Biological Unit (6, 12)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3GOL3Ligand/IonGLYCEROL
4HYP1Mod. Amino Acid4-HYDROXYPROLINE
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:93 , ASN A:95 , GLU A:101 , ASN A:112 , ASP A:113 , MAN A:205BINDING SITE FOR RESIDUE CA A1130
02AC2SOFTWAREGLU A:55 , NAG A:208BINDING SITE FOR RESIDUE NAG A1139
03AC3SOFTWARELYS A:54 , GLU A:55 , ASN A:56 , GLY A:57 , BMA A:202 , MAN A:205 , NAG A:206 , NAG A:207 , HOH A:378 , HOH A:305BINDING SITE FOR RESIDUE NAG A1140
04AC4SOFTWAREGLY A:57 , SER A:61 , PHE A:62 , ASN A:107 , TRP A:108 , MAN A:203 , MAN A:205 , NAG A:208 , HOH A:378 , HOH A:360BINDING SITE FOR RESIDUE BMA A1131
05AC5SOFTWAREGLY A:57 , ASP A:58 , BMA A:202 , NAG A:204 , HOH A:325 , HOH A:392 , HOH A:345 , HOH A:355BINDING SITE FOR RESIDUE MAN A1132
06AC6SOFTWARELYS A:20 , TRP A:108 , MAN A:203 , HOH A:344BINDING SITE FOR RESIDUE NAG A1133
07AC7SOFTWAREPHE A:62 , GLU A:93 , ASN A:95 , GLU A:101 , ASN A:112 , ASP A:113 , ARG A:115 , CA A:201 , BMA A:202 , NAG A:206 , NAG A:208 , HOH A:305BINDING SITE FOR RESIDUE MAN A1134
08AC8SOFTWAREGLU A:93 , ASN A:95 , SER A:97 , MAN A:205 , NAG A:208 , HOH A:378BINDING SITE FOR RESIDUE NAG A1135
09AC9SOFTWAREGLU A:39 , ASP A:41 , TRP A:77 , SER A:80 , ALA A:82 , HOH A:320 , HOH A:376BINDING SITE FOR RESIDUE GOL A1136
10BC1SOFTWAREALA A:32 , TRP A:75 , ALA A:83 , PHE A:84 , LEU A:87 , ARG A:126 , HOH A:374 , HOH A:388 , HOH A:309 , HOH A:385BINDING SITE FOR RESIDUE GOL A1137
11BC2SOFTWAREGLN A:27 , GLN A:31 , ILE A:36 , VAL A:71 , GLN A:76 , SER A:78 , SER A:79 , HOH A:314BINDING SITE FOR RESIDUE GOL A1138

(-) 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 2VUZ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VUZ)

(-) 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-2vuzA01 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
                 2vuz A   1 GCPDGWTQFLDLCYIYQSAKASWASAQSSCQALGGILAEPDTACENEVLIHMCKENGDAGSFGPWLGGQKVGGAWQWSSSGAAFDYLRWGpNEPNNSGGNEDCLHYNWLSWNDLRCHYQASYLCQRAAE 129
                                    10        20        30        40        50        60        70        80        90|      100       110       120         
                                                                                                                     91-HYP
   Legend:   → Mismatch (orange background)
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  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 2VUZ)

(-) CATH Domains  (0, 0)

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

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        Q3KVL7_9BIVA | Q3KVL7: 2vuv

(-) Related Entries Specified in the PDB File

2vuv CRYSTAL STRUCTURE OF CODAKINE AT 1.3A RESOLUTION