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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SOYBEAN AGGLUTININ IN A COMPLEX WITH A BIANTENNARY BLOOD GROUP ANTIGEN ANALOG
 
Authors :  L. Buts, T. W. Hamelryck, M. -H. Dao-Thi, R. Loris, L. Wyns, M. E. Etzler
Date :  23 Nov 00  (Deposition) - 13 Jun 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Jelly-Roll Fold, Legume Lectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Buts, M. H. Dao-Thi, R. Loris, L. Wyns, M. Etzler, T. Hamelryck
Weak Protein-Protein Interactions In Lectins: The Crystal Structure Of A Vegetative Lectin From The Legume Dolichos Biflorus.
J. Mol. Biol. V. 309 193 2001
PubMed-ID: 11491289  |  Reference-DOI: 10.1006/JMBI.2001.4639
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LECTIN
    Chains: A
    Organ: SEED
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Synonym: AGGLUTININ, SBA

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GAL3Ligand/IonBETA-D-GALACTOSE
3MN1Ligand/IonMANGANESE (II) ION
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 28)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GAL12Ligand/IonBETA-D-GALACTOSE
3MN-1Ligand/IonMANGANESE (II) ION
4NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:9 , ASN A:75 , PRO A:182 , LEU A:224 , SER A:225 , NAG A:258BINDING SITE FOR RESIDUE NAG A 256
2AC2SOFTWARELYS A:31 , NAG A:256BINDING SITE FOR RESIDUE NAG A 258
3AC3SOFTWARELEU A:214 , ASP A:215 , GAL A:260 , GAL A:261 , NAG A:262 , GAL A:263BINDING SITE FOR RESIDUE NAG A 259
4AC4SOFTWAREASP A:88 , GLY A:106 , PHE A:128 , ASN A:130 , GLY A:213 , LEU A:214 , ASP A:215 , ILE A:216 , NAG A:259 , NAG A:262 , GAL A:263BINDING SITE FOR RESIDUE GAL A 260
5AC5SOFTWAREPRO A:135 , NAG A:259 , NAG A:262BINDING SITE FOR RESIDUE GAL A 261
6AC6SOFTWARELEU A:214 , ASP A:215 , NAG A:259 , GAL A:260 , GAL A:261 , GAL A:263BINDING SITE FOR RESIDUE NAG A 262
7AC7SOFTWAREASP A:88 , ALA A:105 , GLY A:106 , PHE A:128 , ASN A:130 , LEU A:214 , ASP A:215 , NAG A:259 , GAL A:260 , NAG A:262BINDING SITE FOR RESIDUE GAL A 263
8AC8SOFTWAREGLU A:124 , ASP A:126 , ASP A:133 , HIS A:138 , HOH A:264 , HOH A:265BINDING SITE FOR RESIDUE MN A 254
9AC9SOFTWAREASP A:126 , PHE A:128 , ASN A:130 , ASP A:133 , HOH A:266 , HOH A:267BINDING SITE FOR RESIDUE CA A 255

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G9F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:87 -Asp A:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G9F)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC_SOYBN153-159  1A:121-127
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC_SOYBN232-241  1A:200-209
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC_SOYBN153-159  4A:121-127
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC_SOYBN232-241  4A:200-209

(-) Exons   (0, 0)

(no "Exon" information available for 1G9F)

(-) 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:241
 aligned with LEC_SOYBN | P05046 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:251
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 
            LEC_SOYBN    33 AETVSFSWNKFVPKQPNMILQGDAIVTSSGKLQLNKVDENGTPKPSSLGRALYSTPIHIWDKETGSVASFAASFNFTFYAPDTKRLADGLAFFLAPIDTKPQTHAGYLGLFNENESGDQVVAVEFDTFRNSWDPPNPHIGINVNSIRSIKTTSWDLANNKVAKVLITYDASTSLLVASLVYPSQRTSNILSDVVDLKTSLPEWVRIGFSAATGLDIPGESHDVLSWSFASNLPHASSNIDPLDLTSFVLHE 283
               SCOP domains d1g9fa_ A: Legume lectin                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1g9fA00 A:1-251  [code=2.60.120.200, n   o name defined]                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee................---......eeeeee...ee..........eeeeeeeeeee........eeeeeeeee.......hhhhh............eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeeee.........eeeeeeeeee.......eeeeeeeeeeeee..-------..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------LECTIN_------------------------------------------------------------------------LECTIN_LEG------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g9f A   1 AETVSFSWNKFVPKQPNMILQGDAIVTSSGKLQLNKVD---TPKPSSLGRALYSTPIHIWDKETGSVASFAASFNFTFYAPDTKRLADGLAFFLAPIDTKPQTHAGYLGLFNENESGDQVVAVEFDTFRNSWDPPNPHIGINVNSIRSIKTTSWDLANNKVAKVLITYDASTSLLVASLVYPSQRTSNILSDVVDLKTSLPEWVRIGFSAATGLDIPGESHDVLSWSFASNLPH-------LDLTSFVLHE 251
                                    10        20        30       | - |      50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   |     - |     250 
                                                                38  42                                                                                                                                                                                             234     242
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G9F)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (LEC_SOYBN | P05046)
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.

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    Ala A:87 - Asp A:88   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        LEC_SOYBN | P05046: 1sbd 1sbe 1sbf 2sba 4d69

(-) Related Entries Specified in the PDB File

1sbd ISOMERIC LIGAND
1sbf ISOMERIC LIGAND
2sba ISOMERIC LIGAND