Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60168.13 
• Atom Count: 4175 
• Residue Count: 510 
• Unique protein chains: 1

2G7C

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

• DOI: 10.2210/pdb2G7C/pdb

• Classification: TOXIN
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli


• Deposited: 2006-02-28 Released: 2006-04-18 
• Deposition Author(s): Greco, A., Ho, J.G.S., Lin, S.J., Palcic, M.M., Rupnik, M., Ng, K.K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.236 
• R-Value Work: 0.195 

Literature

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

• PubMed: 16622409 
• DOI: 10.1038/nsmb1084


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Toxin A	A, B	255	Clostridioides difficile	Mutation(s): 0  Gene Names: toxA (tcdA) EC: 3.4.22.-
Find proteins for P16154 (Clostridioides difficile) Go to UniProtKB:  P16154

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
GAL	A, B	BETA-D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLA	A, B	ALPHA D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.236 
• R-Value Work: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 38.682	α = 90.00
b = 132.825	β = 100.29
c = 65.917	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
PHASER	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-28 
• Released Date: 2006-04-18 
• Deposition Author(s): Greco, A., Ho, J.G.S., Lin, S.J., Palcic, M.M., Rupnik, M., Ng, K.K.S.

Revision History 

• Version 1.0: 2006-04-18
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance