SMTL ID : 3pa8.1

Structure of the C. difficile TcdB cysteine protease domain in complex with a peptide inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 621: N-acetylglycyl-N-[(3S)-1-hydroxy-5-methyl-2-oxohexan-3-yl]-L-serinamide(Covalent)

621.1: 12 residues within 4Å: Chain A: I.46, G.109, H.110, G.111, L.153, G.154, C.155, E.200, V.201, R.202, I.203, W.218 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.46, A:V.201 Hydrogen bonds: A:H.110, A:G.111, A:C.155, A:E.200, A:V.201, A:V.201, A:R.202 Water bridges: A:I.203 621.5: 11 residues within 4Å: Chain B: I.46, G.109, H.110, G.111, L.153, G.154, C.155, E.200, V.201, R.202, W.218 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.46, B:V.201 Hydrogen bonds: B:G.111, B:C.155, B:E.200, B:V.201

1 x CA: CALCIUM ION(Non-functional Binders)

CA.2: 2 residues within 4Å: Ligands: IHP.4, IHP.7 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: R.208, K.221 Ligands: IHP.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.208, A:R.208 NA.6: 3 residues within 4Å: Chain B: R.209, K.221 Ligands: IHP.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.209, B:R.209 Water bridges: B:R.209, B:S.231

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.4: 16 residues within 4Å: Chain A: R.28, R.32, Y.34, L.54, K.57, K.104, G.207, R.208, R.209, K.221, K.232, Y.234, K.249 Ligands: CA.2, NA.3, IHP.7 38 PLIP interactions: 38 interactions with chain A Hydrogen bonds: A:R.28, A:R.32, A:Y.34, A:Y.34, A:N.151, A:R.209, A:Y.234 Water bridges: A:K.57, A:K.102, A:K.102, A:K.104, A:K.104, A:R.209, A:R.209, A:K.221, A:K.221, A:S.231, A:S.231, A:K.232, A:K.232, A:K.249, A:K.249 Salt bridges: A:R.28, A:R.32, A:K.57, A:K.57, A:K.102, A:K.104, A:K.104, A:R.208, A:R.209, A:K.221, A:K.221, A:K.221, A:K.232, A:K.249, A:K.249, A:K.249 IHP.7: 17 residues within 4Å: Chain B: R.28, R.32, Y.34, L.54, K.57, K.104, N.151, G.207, R.208, R.209, K.221, K.232, Y.234, K.249 Ligands: CA.2, IHP.4, NA.6 41 PLIP interactions: 40 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.28, B:R.32, B:N.151, B:R.209, B:Y.234 Water bridges: B:R.32, B:H.36, B:K.57, B:K.104, B:R.208, B:R.208, B:R.209, B:K.221, B:K.221, B:K.221, B:K.221, B:S.231, B:K.232, B:K.232, B:K.232, B:K.232, B:K.249, B:K.249, A:S.30 Salt bridges: B:R.28, B:R.32, B:R.32, B:K.57, B:K.57, B:K.102, B:K.104, B:K.104, B:R.208, B:R.209, B:K.221, B:K.221, B:K.221, B:K.232, B:K.249, B:K.249, B:K.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Puri, A.W. et al., Rational design of inhibitors and activity-based probes targeting Clostridium difficile virulence factor TcdB. Chem.Biol. (2010)

Release Date

2010-12-15

Peptides

Toxin B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toxin B

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