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(-) Description

Title :  CRYSTAL STRUCTURE OF CAENORHABDITIS ELEGANS GALECTIN LEC-6
 
Authors :  H. Makyio, T. Takeuchi, M. Tamura, K. Nishiyama, H. Takahashi, H. Natsu Y. Arata, K. Kasai, Y. Yamada, S. Wakatsuki, R. Kato
Date :  10 Jul 12  (Deposition) - 22 May 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Galectin, Galactose-1, 4-Fucose Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Makyio, T. Takeuchi, M. Tamura, K. Nishiyama, H. Takahashi, H. Natsugari, Y. Arata, K. Kasai, Y. Yamada, S. Wakatsuki, R. Kato
Structural Basis Of Preferential Binding Of Fucose-Containing Saccharide By The Caenorhabditis Elegans Galectin Lec-6
Glycobiology V. 23 797 2013
PubMed-ID: 23481096  |  Reference-DOI: 10.1093/GLYCOB/CWT017

(-) Compounds

Molecule 1 - PROTEIN LEC-6
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LEC-6
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: GALECTIN LEC-6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:43 , ASP A:44 , HOH A:435 , HOH A:447BINDING SITE FOR RESIDUE MG A 203
2AC2SOFTWAREMG B:204 , HOH B:308 , HOH B:309BINDING SITE FOR RESIDUE MG B 203
3AC3SOFTWAREMG B:203 , HOH B:309 , HOH B:317BINDING SITE FOR RESIDUE MG B 204
4AC4SOFTWAREHIS A:60 , ASN A:62 , ARG A:64 , GLU A:67 , ASN A:73 , GLU A:83 , HOH A:323 , HOH A:340 , HOH A:352 , HOH A:420 , HOH A:462BINDING SITE FOR LINKED RESIDUES A 201 to 202
5AC5SOFTWAREGLN A:81 , SER A:82 , ARG A:122 , HOH A:411 , HIS B:60 , ASN B:62 , ARG B:64 , GLU B:67 , ASN B:73 , TRP B:80 , GLU B:83 , ARG B:85 , HOH B:319 , HOH B:337 , HOH B:368 , HOH B:399 , HOH B:404BINDING SITE FOR LINKED RESIDUES B 201 to 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VV1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:19 -Pro A:20
2Thr B:19 -Pro B:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VV1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VV1)

(-) Exons   (0, 0)

(no "Exon" information available for 3VV1)

(-) 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:141
 aligned with Q9N384_CAEEL | Q9N384 from UniProtKB/TrEMBL  Length:146

    Alignment length:141
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145 
         Q9N384_CAEEL     6 IGISFRNEFFNPQTPVNIPVQGFSNGARLRLVLLPTSADSRFHINLRTPDDIVLHFNARFDEGAVVNNSTSGGGWQSEDRHANPFQQNKIYTLEFVSNGGIISIFVNGAHFADFVERTPSHGVHLIEIEGGVHVHSAHVSH 146
               SCOP domains d3vv1a_ A: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eee.....eeee.......eeeeeeeee.....eeeeeee....eeeeeeee....eeeee.ee..ee...eee.........eeeeeeee..eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vv1 A   6 IGISFRNEFFNPQTPVNIPVQGFSNGARLRLVLLPTSADSRFHINLRTPDDIVLHFNARFDEGAVVNNSTSGGGWQSEDRHANPFQQNKIYTLEFVSNGGIISIFVNGAHFADFVERTPSHGVHLIEIEGGVHVHSAHVSH 146
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145 


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with Q9N384_CAEEL | Q9N384 from UniProtKB/TrEMBL  Length:146

    Alignment length:140
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146
         Q9N384_CAEEL     7 GISFRNEFFNPQTPVNIPVQGFSNGARLRLVLLPTSADSRFHINLRTPDDIVLHFNARFDEGAVVNNSTSGGGWQSEDRHANPFQQNKIYTLEFVSNGGIISIFVNGAHFADFVERTPSHGVHLIEIEGGVHVHSAHVSH 146
               SCOP domains d3vv1b_ B: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.....eeeeee......eeeeeeee.....eeeeeee....eeeeeeee....eeeee.ee..ee...eee.........eeeeeee...eeeeee..eeeeeee.........eeeeee.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vv1 B   7 GISFRNEFFNPQTPVNIPVQGFSNGARLRLVLLPTSADSRFHINLRTPDDIVLHFNARFDEGAVVNNSTSGGGWQSEDRHANPFQQNKIYTLEFVSNGGIISIFVNGAHFADFVERTPSHGVHLIEIEGGVHVHSAHVSH 146
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146
   Legend:   → Mismatch (orange background)
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VV1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VV1)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9N384_CAEEL | Q9N384)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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