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)

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18177
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHP (Subject of Investigation/LOI) Query on IHP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-03

Deposition Author(s):

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 (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.