SMTL ID : 6v1s.1

Structure of the Clostridioides difficile transferase toxin

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-1-mer

Ligands

14 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.222, D.224, E.231, N.260, E.263, S.264, D.273 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.222, A:E.231, A:N.260, A:E.263, A:D.273 CA.2: 5 residues within 4Å: Chain A: D.220, D.222, D.224, I.226, E.231 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.222, A:D.222, A:D.224, A:I.226, A:E.231 CA.3: 6 residues within 4Å: Chain B: D.222, D.224, E.231, N.260, E.263, D.273 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.222, B:E.231, B:N.260, B:E.263, B:D.273 CA.4: 6 residues within 4Å: Chain B: T.221, D.222, D.224, I.226, P.227, E.231 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.222, B:I.226 CA.5: 7 residues within 4Å: Chain C: D.224, E.231, N.260, E.263, S.264, D.273 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.224, C:E.231, C:N.260, C:E.263, C:D.273 CA.6: 4 residues within 4Å: Chain C: D.224, E.231, E.263 Ligands: CA.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.224, C:D.224 CA.7: 6 residues within 4Å: Chain D: D.222, D.224, E.231, N.260, E.263, D.273 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.222, D:D.224, D:N.260, D:E.263, D:D.273 CA.8: 5 residues within 4Å: Chain D: D.220, D.222, D.224, I.226, E.231 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.220, D:D.222, D:D.224, D:I.226, D:E.231 CA.9: 6 residues within 4Å: Chain E: D.222, D.224, E.231, N.260, E.263, D.273 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.222, E:D.224, E:E.231, E:E.263, E:D.273 CA.10: 6 residues within 4Å: Chain E: D.220, D.222, D.224, I.226, D.228, E.231 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.220, E:D.222, E:D.224, E:I.226, E:E.231 CA.11: 7 residues within 4Å: Chain F: D.222, D.224, E.231, N.260, E.263, S.264, D.273 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.224, F:E.231, F:N.260, F:E.263, F:D.273 CA.12: 5 residues within 4Å: Chain F: D.220, D.222, D.224, I.226, E.231 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.220, F:D.222, F:D.224, F:I.226, F:E.231 CA.13: 7 residues within 4Å: Chain G: D.222, D.224, E.231, N.260, E.263, S.264, D.273 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.222, G:D.224, G:E.231, G:E.263, G:D.273 CA.14: 5 residues within 4Å: Chain G: D.220, D.222, D.224, I.226, E.231 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.222, G:D.222, G:D.224, G:I.226, G:E.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sheedlo, M.J. et al., Structural elucidation of theClostridioides difficiletransferase toxin reveals a single-site binding mode for the enzyme. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-03-18

Peptides

ADP-ribosyltransferase binding component: ABCDEFG
ADP-ribosylating binary toxin enzymatic subunit CdtA: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
Z

ADP-ribosyltransferase binding component

ADP-ribosylating binary toxin enzymatic subunit CdtA

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