9BJA

C. difficile Tcdb cysteine protease domain in complex with IP6

• PDB DOI: https://doi.org/10.2210/pdb9BJA/pdb

• Classification: TOXIN
• Organism(s): Clostridioides difficile 342
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-04-25 Released: 2024-07-03 
• Deposition Author(s): Veyron, S., Cummer, R.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Structure-activity relationship of inositol thiophosphate analogs as allosteric activators of Clostridioides difficile Toxin B

Cummer, R., Grosjean, F., Bolteau, R., Vasegh, S.E., Veyron, S., Keogh, L., Trempe, J.-F., Castagner, B.

(2024) ChemRxiv 

• DOI: https://doi.org/10.26434/chemrxiv-2024-2cf6g-v2

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 61.05 kDa 
• Atom Count: 4,220 
• Modelled Residue Count: 497 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin B	A, B	261	Clostridioides difficile 342	Mutation(s): 0  Gene Names: tcdB, toxB EC: 3.4.22
UniProt
Find proteins for P18177 (Clostridioides difficile) Explore P18177  Go to UniProtKB:  P18177

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	C [auth A], D [auth B]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M39BJA

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.051	α = 90
b = 89.171	β = 103.78
c = 67.597	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
BUSTER	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Veyron, S., Cummer, R.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT-173262
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2020-04908

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release