SMTL ID : 8u5d.1

Crystal Structure of C-terminal domain of Clostridium perfringens Enterotoxin in Space Group P 41 21 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

11 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: D.51, L.80, A.81, S.139, I.140, L.141 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.141 Water bridges: A:S.82 ACT.2: 7 residues within 4Å: Chain A: L.104, G.105, D.106, K.109, D.110, H.111 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.109 Hydrogen bonds: A:D.106 Salt bridges: A:H.111 ACT.4: 2 residues within 4Å: Chain A: L.35, N.36 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.36 Hydrogen bonds: A:N.36 Water bridges: A:D.39 ACT.7: 9 residues within 4Å: Chain A: D.86, F.87, N.88, Q.102, L.104, V.125, K.127 Ligands: GOL.11, GOL.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.86 Hydrogen bonds: A:N.88 Water bridges: A:N.88, A:N.88 ACT.8: 4 residues within 4Å: Chain A: R.34, H.67, T.69, Q.121 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.34 ACT.10: 4 residues within 4Å: Chain A: N.92, N.95, N.96, L.97 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.97 Hydrogen bonds: A:L.97 ACT.19: 2 residues within 4Å: Chain B: S.130, S.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.131 ACT.20: 8 residues within 4Å: Chain A: N.44, P.45, A.46 Chain B: S.82, V.85, Y.138, S.139 Ligands: GOL.17 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.85, A:P.45, A:A.46 Hydrogen bonds: B:S.82, B:S.139, A:N.44 Water bridges: B:S.82 ACT.21: 6 residues within 4Å: Chain B: T.38, L.41, N.42, N.48, A.72, K.144 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.144 Water bridges: B:Q.75, B:K.144 ACT.28: 5 residues within 4Å: Chain B: K.63, N.88, Y.90, V.125 Ligands: GOL.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.88 Salt bridges: B:K.63 ACT.29: 5 residues within 4Å: Chain B: D.110, H.111, Y.112 Ligands: GOL.16, GOL.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.112

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: Y.58, I.84, V.85, Y.132, Y.136, P.137, Y.138 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: I.84, S.130, S.131, Y.132 Chain B: P.45 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: G.74, Q.75, K.76, S.116, D.118 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: S.91, N.92, N.93, N.96, V.98 Ligands: GOL.12 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: N.88, Y.90, K.99, Q.102 Ligands: ACT.7 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain A: S.91, N.93, L.100, S.116, L.117, D.118, Y.122 Ligands: GOL.9 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: L.104, G.105, D.106 Ligands: ACT.2 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: W.60, D.86, K.127, A.128, N.129 Ligands: ACT.7 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain A: S.82, K.83, D.110 Chain B: N.44, A.46, L.49 Ligands: ACT.1 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain B: L.104, G.105, D.106, K.109, D.110, H.111 Ligands: GOL.24, ACT.29 Ligand excluded by PLIP GOL.17: 12 residues within 4Å: Chain A: N.44, L.49 Chain B: D.51, L.80, A.81, S.82, D.110, S.139, I.140, L.141 Ligands: ACT.20, GOL.26 Ligand excluded by PLIP GOL.22: 9 residues within 4Å: Chain B: L.26, D.27, L.28, A.29, A.30, K.63, N.65, V.125 Ligands: ACT.28 Ligand excluded by PLIP GOL.23: 1 residues within 4Å: Chain B: F.94 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain B: Q.102, S.103, L.104, H.111, Y.112, V.113 Ligands: GOL.16, ACT.29 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain B: L.100, S.116, L.117, D.118, Y.122 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain A: L.49 Chain B: D.51, L.80, D.110, L.141 Ligands: GOL.17 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain B: A.31, T.32, N.56, Y.58 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain B: L.35, N.36, D.39, A.40, S.43, Y.50 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.18: 3 residues within 4Å: Chain B: S.19, D.20, I.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.20, B:I.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ogbu, C.P. et al., Structural Basis of Clostridium perfringens Enterotoxin Activation and Oligomerization by Trypsin. Toxins (2023)

Release Date

2023-12-20

Peptides

Heat-labile enterotoxin B chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heat-labile enterotoxin B chain

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