Crystal Structure of basic winged bean lectin in complex with Gal-alpha- 1,6 Glc

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

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Structure and sugar-specificity of basic winged-bean lectin: structures of new disaccharide complexes and a comparative study with other known disaccharide complexes of the lectin.

Kulkarni, K.A.Katiyar, S.Surolia, A.Vijayan, M.Suguna, K.

(2008) Acta Crystallogr D Biol Crystallogr 64: 730-737

  • DOI: https://doi.org/10.1107/S0907444908011323
  • Primary Citation of Related Structures:  
    2ZMK, 2ZML, 2ZMN

  • PubMed Abstract: 

    Crystal structures of the complexes of basic winged-bean agglutinin with the disaccharides Galalpha1-4Gal (galabiose), Galalpha1-6Glc (mellibiose) and Galalpha1-4Galbeta-Et have been determined and the complex with Galalpha1-2Gal has been modelled. The interactions of the nonreducing Gal with the lectin at the primary site are the same as those in the known complexes with disaccharides having the alpha1-->3 linkage. The second residue in Galalpha1-4Gal and Galalpha1-6Glc forms a water bridge to the lectin, while the ethyl group in Galalpha1-4Galbeta-Et makes nonpolar interactions. In complexes involving disaccharides with alpha1-3 linkages, which form part of the A and B blood-group substances, the second sugar residue forms a direct hydrogen bond to the variable loop in the binding site of the lectin. This in part explains the specificity of the lectin for the blood-group substances and also the higher affinity of alpha1-->3-linked disaccharides for the lectin compared with disaccharides involving other linkages. Including those reported here, 14 crystal structures involving the lectin, accounting for 54 crystallographically independent subunits, are available. A comparative study of these structures shows that the region involving the curved beta-sheet which nestles the metal ions is relatively rigid. The carbohydrate-binding region is perched on this region. The flat beta-sheet, which is involved in oligomerization and exhibits considerable variability in legume lectins, is relatively flexible. Indeed, the structures of basic winged-bean lectin have been of critical importance in establishing legume lectins as a family of proteins in which small alterations in essentially the same tertiary structure lead to large variations in quaternary association. They have also provided a structural explanation of the blood-group specificity of the lectin.

  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Basic agglutinin
A, B, C, D
241Psophocarpus tetragonolobusMutation(s): 0 
Gene Names: WBAI
Find proteins for O24313 (Psophocarpus tetragonolobus)
Explore O24313 
Go to UniProtKB:  O24313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO24313
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, H, N
Glycosylation Resources
GlyTouCan:  G11971MR
GlyCosmos:  G11971MR
GlyGen:  G11971MR
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
F, I
Glycosylation Resources
GlyTouCan:  G80587NA
GlyCosmos:  G80587NA
GlyGen:  G80587NA
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
G, J, M, O
Glycosylation Resources
GlyTouCan:  G55954SF
GlyCosmos:  G55954SF
GlyGen:  G55954SF
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G18638YB
GlyCosmos:  G18638YB
GlyGen:  G18638YB
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.061α = 90
b = 91.758β = 90
c = 73.57γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary