› 5vqm

X-ray diffraction
2.79Å resolution

Clostridium difficile TcdB-GTD bound to PA41 Fab

Released:
DOI: 10.2210/pdb5vqm/pdb
Model geometry
Fit model/data
PDB entry 5vqm coloured by chain, front view.
PDB entry 5vqm coloured by chain, side view.
PDB entry 5vqm coloured by chain, top view.
Source organisms:
Primary publication:
A neutralizing antibody that blocks delivery of the enzymatic cargo of Clostridium difficile toxin TcdB into host cells.
Kroh HK, Chandrasekaran R, Zhang Z, Rosenthal K, Woods R, Jin X, Nyborg AC, Rainey GJ, Warrener P, Melnyk RA, Spiller BW, Lacy DB
J Biol Chem 293 941-952 (2018)
PMID: 29180448

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-166226 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Toxin B Chains: A, B
Molecule details ›
Chains: A, B
Length: 557 amino acids
Theoretical weight: 64.54 KDa
Source organism: Clostridioides difficile R20291
Expression system: Priestia megaterium
Structure domains:
Ig-like domain-containing protein Chains: C, L
Molecule details ›
Chains: C, L
Length: 214 amino acids
Theoretical weight: 23.39 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: Q8TCD0 (Residues: 21-239; Coverage: 98%)
Sequence domains:
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chains: D, H

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2221
Unit cell:
a: 96.13Å b: 251.74Å c: 224.45Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.242 0.24 0.292
Expression systems:
  • Priestia megaterium
  • Cricetulus griseus

Quick links

Citations

8 review citations

Clostridioides difficile toxins: mechanisms of action and antitoxin therapeutics.
Kordus et al. (2022)
7 more

4 mentions without citation

Receptor binding mechanisms of Clostridioides difficile toxin B and implications for therapeutics development.
Chen et al. (2023)
3 more