1F9K

WINGED BEAN ACIDIC LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Carbohydrate specificity and salt-bridge mediated conformational change in acidic winged bean agglutinin.

Manoj, N.Srinivas, V.R.Surolia, A.Vijayan, M.Suguna, K.

(2000) J.Mol.Biol. 302: 1129-1137

  • DOI: 10.1006/jmbi.2000.4111
  • Primary Citation of Related Structures:  1FAY
  • Also Cited By: 2D3S

  • PubMed Abstract: 
  • Structures of two crystal forms of the dimeric acidic winged bean agglutinin (WBAII) complexed with methyl-alpha-D-galactose have been determined at 3.0 A and 3.3 A resolution. The subunit structure and dimerisation of the lectin are similar to those ...

    Structures of two crystal forms of the dimeric acidic winged bean agglutinin (WBAII) complexed with methyl-alpha-D-galactose have been determined at 3.0 A and 3.3 A resolution. The subunit structure and dimerisation of the lectin are similar to those of the basic lectin from winged bean (WBAI) and the lectin from Erythrina corallodendron (EcorL). The conformation of a loop and its orientation with respect to the rest of the molecule in WBAII are, however, different from those in all the other legume lectins of known structure. This difference appears to have been caused by the formation of two strategically placed salt bridges in the former. Modelling based on the crystal structures provides a rationale for the specificity of the lectin, which is very different from that of WBAI, for the H-antigenic determinant responsible for O blood group reactivity. It also leads to a qualitative explanation for the thermodynamic data on sugar-binding to the lectin, with special emphasis on the role of a tyrosyl residue in the variable loop in the sugar-binding region in generating the carbohydrate specificity of WBAII.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Analysis of Winged Bean Acidic Lectin
      Manoj, N.,Srinivas, V.R.,Satish, B.,Singha, N.C.,Suguna, K.
      (1999) Acta Crystallogr.,Sect.D 55: 564


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACIDIC LECTIN
A, B
238Psophocarpus tetragonolobusGene Names: wba2
Find proteins for Q9SM56 (Psophocarpus tetragonolobus)
Go to UniProtKB:  Q9SM56
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
AMG
Query on AMG

Download SDF File 
Download CCD File 
A
ALPHA-METHYL-D-GALACTOSIDE
C7 H14 O6
HOVAGTYPODGVJG-PZRMXXKTSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 182.110α = 90.00
b = 182.110β = 90.00
c = 44.990γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance