1K7U

Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,4GlcNAc complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interactions of wheat-germ agglutinin with GlcNAc beta 1,6Gal sequence

Muraki, M.Ishimura, M.Harata, K.

(2002) Biochim.Biophys.Acta 1569: 10-20

  • Primary Citation of Related Structures:  1K7T, 1K7V

  • PubMed Abstract: 
  • The interactions of wheat-germ agglutinin (WGA) with the GlcNAc beta 1,6Gal sequence, a characteristic component of branched poly-N-acetyllactosaminoglycans, were investigated using isothermal titration calorimetry and X-ray crystallography. GlcNAc b ...

    The interactions of wheat-germ agglutinin (WGA) with the GlcNAc beta 1,6Gal sequence, a characteristic component of branched poly-N-acetyllactosaminoglycans, were investigated using isothermal titration calorimetry and X-ray crystallography. GlcNAc beta 1,6Gal exhibited an affinity greater than GlcNAc beta 1,4GlcNAc to all WGA isolectins, whereas Gal beta 1,6GlcNAc showed much less affinity than GlcNAc beta 1,4GlcNAc. X-ray structural analyses of the glutaraldehyde-crosslinked WGA isolectin 3 crystals in complex with GlcNAc beta 1,6Gal, GlcNAc beta 1,4GlcNAc and GlcNAc beta 1,6Gal beta 1,4Glc were performed at 2.4, 2.2 and 2.2 A resolution, respectively. In spite of different glycosidic linkages, GlcNAc beta 1,6Gal and GlcNAc beta 1,4GlcNAc exhibited basically similar binding modes to each other, in contact with side chains of two aromatic residues, Tyr64 and His66. However, the conformations of the ligands in the two primary binding sites were not always identical. GlcNAc beta 1,6Gal showed more extensive variation in the parameters defining the glycosidic linkage structure compared to GlcNAc beta 1,4GlcNAc, demonstrating large conformational flexibility of the former ligand in the interaction with WGA. The difference in the ligand binding conformation was accompanied by alterations of the side chain conformation of the amino acid residues involved in the interactions. The hydrogen bond between Ser62 and the non-reducing end GlcNAc was always observed regardless of the ligand type, indicating the key role of this interaction. In addition to the hydrogen bonding and van der Waals interactions, CH--pi interactions involving Tyr64, His66 and Tyr73 are suggested to play an essential role in determining the ligand binding conformation in all complexes. One of the GlcNAc beta 1,6Gal ligands had no crystal packing contact with another WGA molecule, therefore the conformation might be more relevant to the interaction mode in solution.


    Related Citations: 
    • X-ray structure of wheat germ agglutinin isolectin 3
      Harata, K.,Nagahora, H.,Jigami, Y.
      (1995) Acta Crystallogr.,Sect.D 51: 1013
    • Chemically prepared hevein domains: effect of C-terminal truncation and the mutagenesis of aromatic residues on the affinity for chitin
      Muraki, M.,Morii, H.,Harata, K.
      (2000) Protein Eng. 13: 385
    • Crystal structures of Urtica dioica agglutinin and its complex with tri-N-acetylchitotriose
      Harata, K.,Muraki, M.
      (2000) J.Mol.Biol. 297: 673


    Organizational Affiliation

    Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan. m-muraki@aist.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
agglutinin isolectin 3
A, B
186Triticum aestivumN/A
Find proteins for P10969 (Triticum aestivum)
Go to UniProtKB:  P10969
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.720α = 90.00
b = 91.550β = 110.13
c = 44.760γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
MADNESdata reduction
X-PLORrefinement
Adata reduction
Adata scaling
X-PLORphasing
MADNESdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-03
    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