SMTL ID : 8yvo.1 (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

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

EDO.1: 4 residues within 4Å: Chain A: T.125, D.126, A.127 Chain B: R.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.125, A:A.127 Water bridges: A:D.126 EDO.2: 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.3: 6 residues within 4Å: Chain A: D.120, R.121, H.123 Chain B: V.25, T.26, Q.29 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.26, B:T.26, B:Q.29, A:D.120 EDO.4: 5 residues within 4Å: Chain B: F.8, H.10, I.15, Y.36, D.63 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.63 EDO.5: 1 residues within 4Å: Chain B: L.11 No protein-ligand interaction detected (PLIP)

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
A

B
C

C4.2 nanobody

Toxin A

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