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(-) Description

Title :  CRYSTAL STRUCTURE OF C-TYPE LECTIN CEL-I FROM CUCUMARIA ECHINATA
 
Authors :  H. Sugawara, M. Kusunoki, G. Kurisu, T. Fujimoto, H. Aoyagi, T. Hatakey
Date :  22 Jul 04  (Deposition) - 07 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  C-Type Lectin, N-Acetylgalactosamine, Invertebrate, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Sugawara, M. Kusunoki, G. Kurisu, T. Fujimoto, H. Aoyagi, T. Hatakeyama
Characteristic Recognition Of N-Acetylgalactosamine By An Invertebrate C-Type Lectin, Cel-I, Revealed By X-Ray Crystallographic Analysis
J. Biol. Chem. V. 279 45219 2004
PubMed-ID: 15319425  |  Reference-DOI: 10.1074/JBC.M408840200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LECTIN CEL-I, N-ACETYL-D-GALACTOSAMINE-SPECIFIC C-TYPE
    Chains: A, B
    Organism Scientific: CUCUMARIA ECHINATA
    Organism Taxid: 40245
    Synonym: C-TYPE LECTIN, CEL-I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:77 , GLU A:81 , ASN A:104 , GLU A:109 , ASP A:110 , HOH A:320BINDING SITE FOR RESIDUE CA A 201
2AC2SOFTWAREGLN A:101 , ASP A:103 , GLU A:109 , ASN A:123 , ASP A:124 , MPD A:301BINDING SITE FOR RESIDUE CA A 202
3AC3SOFTWAREGLU A:81 , ASP A:110 , HOH A:321 , HOH A:354 , HOH A:376 , GLY B:93BINDING SITE FOR RESIDUE CA A 203
4AC4SOFTWAREASP B:77 , GLU B:81 , ASN B:104 , GLU B:109 , ASP B:110 , HOH B:322BINDING SITE FOR RESIDUE CA B 201
5AC5SOFTWAREGLN B:101 , ASP B:103 , GLU B:109 , ASN B:123 , ASP B:124 , MPD B:302BINDING SITE FOR RESIDUE CA B 202
6AC6SOFTWAREGLU B:81 , ASP B:110 , HOH B:323 , HOH B:355 , HOH B:421BINDING SITE FOR RESIDUE CA B 203
7AC7SOFTWAREGLN A:101 , ASP A:103 , GLU A:109 , ASN A:123 , ASP A:124 , CA A:202BINDING SITE FOR RESIDUE MPD A 301
8AC8SOFTWAREGLN B:101 , ASP B:103 , TRP B:105 , GLU B:109 , ASN B:123 , ASP B:124 , CA B:202BINDING SITE FOR RESIDUE MPD B 302

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:3 -A:14
2A:31 -A:135
3A:36 -B:36
4B:3 -B:14
5B:31 -B:135

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:101 -Pro A:102
2Gln B:101 -Pro B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WMY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WMY)

(-) Exons   (0, 0)

(no "Exon" information available for 1WMY)

(-) 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:140
 aligned with Q7M462_CUCEC | Q7M462 from UniProtKB/TrEMBL  Length:140

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
         Q7M462_CUCEC     1 NQCPTDWEAEGDHCYRFFNTLTTWENAHHECVSYSCSTLNVRSDLVSVHSAAEQAYVFNYWRGIDSQAGQLWIGLYDKYNEGDFIWTDGSKVGYTKWAGGQPDNWNNAEDYGQFRHTEGGAWNDNSAAAQAKYMCKLTFE 140
               SCOP domains d1wmya_ A: Lectin CEL-I                                                                                                                      SCOP domains
               CATH domains 1wmyA00 A:1-140 Mannose-Binding Protein A, subunit A                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eeeeeeeeeehhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhh....eeeeeee........ee.................hhhhh..eeeee......eeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmy A   1 NQCPTDWEAEGDHCYRFFNTLTTWENAHHECVSYSCSTLNVRSDLVSVHSAAEQAYVFNYWRGIDSQAGQLWIGLYDKYNEGDFIWTDGSKVGYTKWAGGQPDNWNNAEDYGQFRHTEGGAWNDNSAAAQAKYMCKLTFE 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with Q7M462_CUCEC | Q7M462 from UniProtKB/TrEMBL  Length:140

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
         Q7M462_CUCEC     1 NQCPTDWEAEGDHCYRFFNTLTTWENAHHECVSYSCSTLNVRSDLVSVHSAAEQAYVFNYWRGIDSQAGQLWIGLYDKYNEGDFIWTDGSKVGYTKWAGGQPDNWNNAEDYGQFRHTEGGAWNDNSAAAQAKYMCKLTFE 140
               SCOP domains d1wmyb_ B: Lectin CEL-I                                                                                                                      SCOP domains
               CATH domains 1wmyB00 B:1-140 Mannose-Binding Protein A, subunit A                                                                                         CATH domains
           Pfam domains (1) -------------------Lectin_C-1wmyB01 B:20-137                                                                                             --- Pfam domains (1)
           Pfam domains (2) -------------------Lectin_C-1wmyB02 B:20-137                                                                                             --- Pfam domains (2)
         Sec.struct. author .......eee..eeeeeeeeeehhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhh.....eeeeee........ee.................hhhh.eeeeee..hhhh.eeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmy B   1 NQCPTDWEAEGDHCYRFFNTLTTWENAHHECVSYSCSTLNVRSDLVSVHSAAEQAYVFNYWRGIDSQAGQLWIGLYDKYNEGDFIWTDGSKVGYTKWAGGQPDNWNNAEDYGQFRHTEGGAWNDNSAAAQAKYMCKLTFE 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: C_Lectin (98)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7M462_CUCEC | Q7M462)
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
        Q7M462_CUCEC | Q7M462: 1wmz 4wqq

(-) Related Entries Specified in the PDB File

1bch C-TYPE LECTIN COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE
1bcj C-TYPE LECTIN COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE
1byf INVERTEBRATE C-TYPE LECTIN
1tlg INVERTEBRATE C-TYPE LECTIN
1wmz THE SAME PROTEIN COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE