2DTW

Crystal Structure of basic winged bean lectin in complex with 2Me-O-D-Galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for the carbohydrate-specificity of basic winged-bean lectin and its differential affinity for Gal and GalNAc

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

(2006) ACTA CRYSTALLOGR.,SECT.D 62: 1319-1324

  • DOI: 10.1107/S0907444906028198
  • Primary Citation of Related Structures:  
  • Also Cited By: 2ZMN, 2E7T, 2E7Q, 2E53, 2E51

  • PubMed Abstract: 
  • The crystal structure of the complexes of basic winged-bean lectin with galactose, 2-methoxygalactose, N-acetylgalactosamine and methyl-alpha-N-acetylgalactosamine have been determined. Lectin-sugar interactions involve four hydrogen bonds and a stac ...

    The crystal structure of the complexes of basic winged-bean lectin with galactose, 2-methoxygalactose, N-acetylgalactosamine and methyl-alpha-N-acetylgalactosamine have been determined. Lectin-sugar interactions involve four hydrogen bonds and a stacking interaction in all of the complexes. In addition, an N-H...O hydrogen bond involving the hydroxyl group at C2 exists in the galactose and 2-methoxygalactose complexes. An additional hydrophobic interaction involving the methyl group in the latter leads to the higher affinity of the methyl derivative. In the lectin-N-acetylgalactosamine complex the N-H...O hydrogen bond is lost, but a compensatory hydrogen bond is formed involving the O atom of the acetamido group. In addition, the CH(3) moiety of the acetamido group is involved in hydrophobic interactions. Consequently, the 2-methyl and acetamido derivatives of galactose have nearly the same affinity for the lectin. The methyl group alpha-linked to the galactose takes part in additional hydrophobic interactions. Therefore, methyl-alpha-N-acetylgalactosamine has a higher affinity than N-acetylgalactosamine for the lectin. The structures of basic winged-bean lectin-sugar complexes provide a framework for examining the relative affinity of galactose and galactosamine for the lectins that bind to them. The complexes also lead to a structural explanation for the blood-group specificity of basic winged-bean lectin.


    Related Citations: 
    • Carbohydrate specificity and quaternary association in basic winged bean lectin: X-ray analysis of the lectin at 2.5 A resolution
      Prabu, M.M.,Sankaranarayanan, R.,Puri, K.D.,Sharma, V.,Surolia, A.,Vijayan, M.,Suguna, K.
      (1998) J.Mol.Biol. 276: 787
    • Structural basis for the specificity of basic winged bean lectin for the Tn-antigen: a crystallographic, thermodynamic and modelling study
      Kulkarni, K.A.,Sinha, S.,Katiyar, S.,Surolia, A.,Vijayan, M.,Suguna, K.
      (2005) Febs Lett. 579: 6775


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Basic agglutinin
A, B, C, D
241Psophocarpus tetragonolobusMutation(s): 0 
Gene Names: WBAI
Find proteins for O24313 (Psophocarpus tetragonolobus)
Go to UniProtKB:  O24313
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
2GS
Query on 2GS

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Download CCD File 
A, B, C, D
2-O-METHYL-ALPHA-D-GALACTOPYRANOSE
C7 H14 O6
UMPNFVHHMOSNAC-PZRMXXKTSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A, B, C, D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUL
Query on FUL

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Download CCD File 
C
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 157.431α = 90.00
b = 91.061β = 90.00
c = 73.383γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data reduction
SCALEPACKdata scaling
MAR345data collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description