Clostridium difficile Toxin A Fragment Bound to aGal(1,3)bGal(1,4)bGlcNAc

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

This is version 2.2 of the entry. See complete history


Carbohydrate recognition by Clostridium difficile toxin A.

Greco, A.Ho, J.G.Lin, S.J.Palcic, M.M.Rupnik, M.Ng, K.K.

(2006) Nat Struct Mol Biol 13: 460-461

  • DOI: https://doi.org/10.1038/nsmb1084
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Clostridium difficile TcdA is a large toxin that binds carbohydrates on intestinal epithelial cells. A 2-A resolution cocrystal structure reveals two molecules of alpha-Gal-(1,3)-beta-Gal-(1,4)-beta-GlcNAcO(CH(2))(8)CO(2)CH(3) binding in an extended conformation to TcdA. Residues forming key contacts with the trisaccharides are conserved in all seven putative binding sites in TcdA, suggesting a mode of multivalent binding that may be exploited for the rational design of novel therapeutics.

  • Organizational Affiliation

    Alberta Ingenuity Centre for Carbohydrate Science, University of Calgary, Calgary, Canada T2N 1N4.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin A
A, B
255Clostridioides difficileMutation(s): 14 
Gene Names: toxAtcdA
Find proteins for P16154 (Clostridioides difficile)
Explore P16154 
Go to UniProtKB:  P16154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16154
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D, E, F
Glycosylation Resources
GlyTouCan:  G03499BP
GlyCosmos:  G03499BP
GlyGen:  G03499BP
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.682α = 90
b = 132.825β = 100.29
c = 65.917γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 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: 2022-12-21
    Changes: Database references, Structure summary
  • Version 2.2: 2023-09-20
    Changes: Data collection, Refinement description