SMTL ID : 9bja.1

C. difficile Tcdb cysteine protease domain in complex with IP6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 12 residues within 4Å: Chain A: R.33, Y.35, L.55, K.58, K.105, N.152, R.209, R.210, K.222, K.233, Y.235, K.250 32 PLIP interactions: 32 interactions with chain A Hydrogen bonds: A:R.33, A:Y.35, A:Y.35, A:N.152, A:R.210, A:R.210, A:Y.235 Water bridges: A:R.33, A:R.209, A:R.209, A:R.210, A:R.210, A:K.222, A:K.222, A:S.232, A:K.233, A:K.233 Salt bridges: A:R.33, A:K.58, A:K.58, A:K.103, A:K.105, A:K.105, A:R.209, A:R.210, A:K.222, A:K.222, A:K.222, A:K.233, A:K.250, A:K.250, A:K.250 IHP.2: 13 residues within 4Å: Chain B: R.33, Y.35, L.55, K.58, K.105, N.152, G.208, R.209, R.210, K.222, K.233, Y.235, K.250 33 PLIP interactions: 33 interactions with chain B Hydrogen bonds: B:R.33, B:R.33, B:Y.35, B:N.152, B:R.210, B:Y.235, B:Y.235 Water bridges: B:K.58, B:K.105, B:K.105, B:R.209, B:R.209, B:R.210, B:R.210, B:S.232, B:K.233, B:K.233 Salt bridges: B:R.33, B:R.33, B:K.58, B:K.58, B:K.103, B:K.105, B:K.105, B:R.209, B:R.210, B:K.222, B:K.222, B:K.222, B:K.233, B:K.250, B:K.250, B:K.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cummer, R. et al., Structure-activity relationship of inositol thiophosphate analogs as allosteric activators of Clostridioides difficile Toxin B. Chemrxiv (2024)

Release Date

2024-07-03

Peptides

Toxin B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toxin B