1JOT

STRUCTURE OF THE LECTIN MPA COMPLEXED WITH T-ANTIGEN DISACCHARIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the complex of Maclura pomifera agglutinin and the T-antigen disaccharide, Galbeta1,3GalNAc.

Lee, X.Thompson, A.Zhang, Z.Ton-that, H.Biesterfeldt, J.Ogata, C.Xu, L.Johnston, R.A.Young, N.M.

(1998) J.Biol.Chem. 273: 6312-6318


  • PubMed Abstract: 
  • Maclura pomifera agglutinin is a tetrameric plant seed lectin with high affinity for the tumor-associated T-antigen disaccharide, Galbeta1,3GalNAcalpha, and hence for many O-linked glycopeptide structures. Unlike members of most lectin families, it l ...

    Maclura pomifera agglutinin is a tetrameric plant seed lectin with high affinity for the tumor-associated T-antigen disaccharide, Galbeta1,3GalNAcalpha, and hence for many O-linked glycopeptide structures. Unlike members of most lectin families, it lacks both metal ions and Cys residues. The structure of its complex with Galbeta1,3GalNAc was determined to 2.2 by first using multiwavelength anomalous diffraction with a lead derivative of the native protein, and then using molecular replacement with the unrefined structure as a model to solve the structure of the complex. The subunits share the beta-prism architecture and three-fold pseudo-symmetry of the related lectin jacalin, with the 21-residue beta-chains in the center of the tetramer. Interactions with the GalNAc predominate in the binding of the disaccharide. It forms a network of H-bonds with only one side chain, from an Asp residue, the amino group of the N-terminal Gly of the alpha-chain, and peptide backbone atoms of two aromatic residues. The Gal moiety does not H-bond directly with residues in the same monomer, i.e. there is no true subsite for it, but there are interactions through two water molecules. In the crystal, it interacts with residues in the binding site of an adjacent tetramer. The minimum energy conformation expected for the disaccharide is retained, despite its mediating the tetramer-tetramer interactions in the crystal packing. The resulting lattice is comparable to those seen for complexes of other lectins with branched glycopeptides.


    Organizational Affiliation

    Department of Cancer Biology, Cleveland Clinic Research Institute, Cleveland, Ohio 44195, USA. lee@xtal.ri.ccf.org




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AGGLUTININ
A
133Maclura pomiferaN/A
Find proteins for P18674 (Maclura pomifera)
Go to UniProtKB:  P18674
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AGGLUTININ
B
20Maclura pomiferaN/A
Find proteins for P18676 (Maclura pomifera)
Go to UniProtKB:  P18676
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download SDF File 
Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
A2G
Query on A2G

Download SDF File 
Download CCD File 
A
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.172 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 67.600α = 90.00
b = 67.600β = 90.00
c = 149.260γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
SOFTWAREdata reduction
X-PLORrefinement
HAMLINdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance