› 6oq5

X-ray diffraction
3.87Å resolution

Structure of the full-length Clostridium difficile toxin B in complex with 3 VHHs

Released:
DOI: 10.2210/pdb6oq5/pdb
Model geometry
Fit model/data
PDB entry 6oq5 coloured by chain, front view.
PDB entry 6oq5 coloured by chain, side view.
PDB entry 6oq5 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
OpenAccess logo Nat Struct Mol Biol 26 712-719 (2019)
PMID: 31308519

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-231656 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Peptidase C80 domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 2373 amino acids
Theoretical weight: 270.38 KDa
Source organism: Clostridioides difficile
Expression system: Priestia megaterium
UniProt:
  • Canonical: M4NKV9 (Residues: 1-2367; Coverage: 100%)
Gene names: KRQ00_003159, tcdB, toxB
Sequence domains:
5D Chain: D
Molecule details ›
Chain: D
Length: 153 amino acids
Theoretical weight: 16.86 KDa
Source organism: Camelidae
Expression system: Escherichia coli
E3 Chain: E
7F Chain: F

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 149.619Å b: 168.565Å c: 179.921Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.265 0.263 0.315
Expression systems:
  • Priestia megaterium
  • Escherichia coli

Quick links

Citations

7 review citations

Bezlotoxumab for Preventing Recurrent Clostridioides difficile Infection: A Narrative Review from Pathophysiology to Clinical Studies.
Giacobbe et al. (2020)
6 more

17 mentions without citation

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