SMTL ID : 8yvo.2 (1 other biounit)

Crystal structure of the C. difficile toxin A CROPs domain fragment 2639-2707 bound to C4.2 nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: Y.79, K.84, G.85, R.86, F.87, T.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.85, A:T.88 EDO.2: 3 residues within 4Å: Chain A: Q.58, E.63, R.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.58, A:E.63, A:R.64 EDO.3: 6 residues within 4Å: Chain B: F.8, H.10, I.15, Y.36, D.63, V.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.10, B:Y.36 Water bridges: B:K.34, B:D.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sluchanko, N.N. et al., Structural insight into recognition of Clostridioides difficile toxin A by novel neutralizing nanobodies targeting QTIN-like motifs within its receptor-binding domain. Int.J.Biol.Macromol. (2024)

Release Date

2024-12-18

Peptides

C4.2 nanobody: A
Toxin A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C4.2 nanobody

Toxin A

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