› 6oq6

X-ray diffraction
2.97Å resolution

Structure of the pore forming fragment of Clostridium difficile toxin B in complex with VHH 5D

Released:
DOI: 10.2210/pdb6oq6/pdb
PDB entry 6oq6 coloured by chain, front view.
PDB entry 6oq6 coloured by chain, side view.
PDB entry 6oq6 coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the full-length Clostridium difficile toxin B.
Chen P, Lam KH, Liu Z, Mindlin FA, Chen B, Gutierrez CB, Huang L, Zhang Y, Hamza T, Feng H, Matsui T, Bowen ME, Perry K, Jin R
Nat Struct Mol Biol 26 712-719 (2019)
PMID: 31308519

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-231767 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Toxin B Chain: A
Molecule details ›
Chain: A
Length: 363 amino acids
Theoretical weight: 40.54 KDa
Source organism: Clostridioides difficile
Expression system: Escherichia coli
UniProt:
  • Canonical: P18177 (Residues: 1071-1432; Coverage: 15%)
Gene names: tcdB, toxB
Sequence domains: TcdA/TcdB pore forming domain
5D Chain: D
Molecule details ›
Chain: D
Length: 153 amino acids
Theoretical weight: 16.86 KDa
Source organism: Camelidae
Expression system: Escherichia coli

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P6122
Unit cell:
a: 169.82Å b: 169.82Å c: 79.12Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.26 0.259 0.274
Expression system: Escherichia coli

Quick links

Citations

8 review citations

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

3 mentions without citation

Single Domain Antibody application in bacterial infection diagnosis and neutralization.
Qin et al. (2022)
2 more