› 7uby

X-ray diffraction
2.1Å resolution

Structure of the GTD domain of Clostridium difficile toxin A in complex with VHH AH3

Released:
DOI: 10.2210/pdb7uby/pdb
PDB entry 7uby coloured by chain, front view.
PDB entry 7uby coloured by chain, side view.
PDB entry 7uby coloured by chain, top view.
Source organisms:
Primary publication:
Neutralizing epitopes on Clostridioides difficile toxin A revealed by the structures of two camelid VHH antibodies.
Chen B, Perry K, Jin R
OpenAccess logo Front Immunol 13 978858 (2022)
PMID: 36466927

Function and Biology Details

Biochemical function:
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-233291 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Glucosyltransferase TcdA Chains: A, B
Molecule details ›
Chains: A, B
Length: 543 amino acids
Theoretical weight: 62.92 KDa
Source organism: Clostridioides difficile
Expression system: Escherichia coli
UniProt:
  • Canonical: P16154 (Residues: 1-542; Coverage: 20%)
Gene names: tcdA, toxA
Sequence domains:
Nanobody VHH AH3 Chains: C, D
Molecule details ›
Chains: C, D
Length: 151 amino acids
Theoretical weight: 16.11 KDa
Source organism: Camelidae
Expression system: Escherichia coli

Ligands and Environments

4 bound ligands:
Ligand UPG 2 x UPG
Ligand MN 2 x MN
Ligand PEG 2 x PEG
Ligand EDO 11 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 80.118Å b: 131.641Å c: 83.796Å
α: 90° β: 110.015° γ: 90°
R-values:
R R work R free
0.219 0.218 0.26
Expression system: Escherichia coli

Quick links

Citations

1 review citation

New treatment approaches for Clostridioides difficile infections: alternatives to antibiotics and fecal microbiota transplantation.
Bratkovič et al. (2024)

1 mention without citation

Neutralizing epitopes on Clostridioides difficile toxin A revealed by the structures of two camelid VHH antibodies.
Chen et al. (2022)