SMTL ID : 7ee6.1

Crystal structure of PltC toxin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-5-1-1-mer

Ligands

10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 7 residues within 4Å: Chain A: N.15, N.16, G.35, L.36, N.46 Chain B: Y.112, M.114 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.112, A:N.15, A:N.15, A:N.16 Water bridges: B:Y.112 PEG.5: 7 residues within 4Å: Chain B: Y.54, G.55, K.58, V.86, W.87, R.88 Ligands: ACN.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.55, B:K.58, B:R.88 PEG.15: 8 residues within 4Å: Chain D: S.24, Y.54, G.55, V.86, W.87, R.88, D.89 Ligands: ACN.19 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.24, D:G.55, D:R.88, D:R.88, D:D.89 PEG.16: 7 residues within 4Å: Chain A: Y.112, M.114 Chain D: N.15, N.16, G.35, L.36, N.46 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:Y.112, D:N.15, D:N.16, D:G.35 Water bridges: A:Y.112 PEG.17: 7 residues within 4Å: Chain C: D.91, S.94, A.95 Chain D: A.1, M.2, P.116, T.117 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:M.2, D:T.117, D:T.117 PEG.20: 3 residues within 4Å: Chain E: Y.8, V.9, S.10 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.10, E:S.10 PEG.21: 6 residues within 4Å: Chain B: Y.72 Chain E: G.76, D.77, T.106, C.107 Chain G: Q.176 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:D.77, E:D.77, E:D.77, B:Y.72 Water bridges: E:G.76 PEG.26: 5 residues within 4Å: Chain F: M.8, L.228, R.229, N.230, A.241 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.230 PEG.30: 8 residues within 4Å: Chain E: Y.72, T.73, G.75 Chain G: H.101, F.102, N.103, A.104, K.107 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:T.73, G:A.104 Water bridges: E:G.75, G:K.107 PEG.31: 7 residues within 4Å: Chain G: R.76, K.129, V.131, D.144, G.145, V.146, S.147 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.147 Water bridges: G:S.147, G:S.147

16 x ACN: ACETONE(Non-covalent)

ACN.2: 5 residues within 4Å: Chain A: L.17, S.18, Y.19, L.65 Chain B: T.67 Ligand excluded by PLIP ACN.3: 6 residues within 4Å: Chain A: N.15, K.37, G.39, S.40, E.41, A.42 Ligand excluded by PLIP ACN.6: 7 residues within 4Å: Chain B: S.24, Y.54, W.87, R.88, D.89, F.92 Ligands: PEG.5 Ligand excluded by PLIP ACN.7: 5 residues within 4Å: Chain B: K.37, G.39, S.40, E.41, A.42 Ligand excluded by PLIP ACN.8: 4 residues within 4Å: Chain B: H.38, G.39, S.40, E.41 Ligand excluded by PLIP ACN.9: 4 residues within 4Å: Chain A: Y.72 Chain B: G.76, D.77, C.107 Ligand excluded by PLIP ACN.12: 7 residues within 4Å: Chain C: S.24, Y.54, W.87, R.88, D.89, F.92 Ligands: GOL.13 Ligand excluded by PLIP ACN.18: 6 residues within 4Å: Chain A: T.67 Chain D: L.17, S.18, Y.19, L.65, K.69 Ligand excluded by PLIP ACN.19: 4 residues within 4Å: Chain D: G.55, N.56, R.88 Ligands: PEG.15 Ligand excluded by PLIP ACN.22: 4 residues within 4Å: Chain E: E.84, K.93, S.98, R.99 Ligand excluded by PLIP ACN.32: 5 residues within 4Å: Chain A: T.74 Chain G: G.183, Y.212, V.217 Ligands: ACN.33 Ligand excluded by PLIP ACN.33: 5 residues within 4Å: Chain D: Y.72 Chain G: R.62, G.183, P.184 Ligands: ACN.32 Ligand excluded by PLIP ACN.34: 8 residues within 4Å: Chain F: D.4, Y.5, Q.106 Chain G: R.27, R.46, T.119, L.120, F.167 Ligand excluded by PLIP ACN.35: 6 residues within 4Å: Chain G: Y.94, V.164, I.165, P.166, F.167, L.168 Ligand excluded by PLIP ACN.36: 3 residues within 4Å: Chain G: R.111, L.112, R.114 Ligand excluded by PLIP ACN.37: 3 residues within 4Å: Chain G: R.67, S.68, T.69 Ligand excluded by PLIP

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Y.22, T.23, S.24, G.25, G.26, D.89 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.25, A:G.26, A:D.89 Water bridges: A:Y.22 GOL.10: 7 residues within 4Å: Chain B: N.15, N.16, G.35, L.36, N.46 Chain E: Y.112, M.114 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:N.15, B:N.15, B:N.16 Water bridges: E:Y.112 GOL.11: 3 residues within 4Å: Chain B: D.6, T.7, Y.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.8, B:Y.8 Water bridges: B:Y.8, B:Y.82, B:Y.82 GOL.13: 5 residues within 4Å: Chain C: Y.54, G.55, V.86, R.88 Ligands: ACN.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.55, C:R.88 GOL.14: 7 residues within 4Å: Chain C: N.15, N.16, G.35, L.36, N.46 Chain D: Y.112, M.114 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.15, C:N.16, C:G.35, D:Y.112 GOL.23: 5 residues within 4Å: Chain E: Y.54, G.55, N.56, V.86, R.88 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.55, E:R.88 GOL.24: 7 residues within 4Å: Chain C: Y.112, M.114 Chain E: N.15, N.16, G.35, L.36, N.46 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:Y.112, E:N.15, E:N.15, E:N.16 Water bridges: C:Y.112, C:G.115 GOL.27: 6 residues within 4Å: Chain F: K.6, A.35 Chain G: Y.25, N.26, D.44 Ligands: FLC.25 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:D.44, F:K.6 Water bridges: G:Y.25 GOL.28: 8 residues within 4Å: Chain F: R.164, H.165, L.166, R.218, P.220 Chain G: L.123, P.124, E.125 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:H.165, F:R.218, G:E.125

2 x FLC: CITRATE ANION(Non-covalent)

FLC.25: 9 residues within 4Å: Chain F: T.34, A.35 Chain G: Y.25, N.26, R.27, N.28, P.169, Q.172 Ligands: GOL.27 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:P.169 Hydrogen bonds: G:N.26, G:N.26, G:R.27, G:N.28 Water bridges: G:N.26, G:Q.31 FLC.29: 7 residues within 4Å: Chain D: S.109, S.110 Chain G: S.52, S.53, V.54, N.55, R.114 9 PLIP interactions: 8 interactions with chain G, 1 interactions with chain D Hydrogen bonds: G:S.53, G:S.53, G:V.54, G:N.55, G:R.114, D:S.110 Water bridges: G:N.55, G:N.55 Salt bridges: G:R.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Molecular Insights into the Assembly and Functional Diversification of Typhoid Toxin. Mbio (2022)

Release Date

2021-12-22

Peptides

Subtilase cytotoxin subunit B-like protein: ABCDE
Cytolethal distending toxin subunit B family protein: F
Pertussis-like toxin subunit ArtA: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Subtilase cytotoxin subunit B-like protein

Cytolethal distending toxin subunit B family protein

Pertussis-like toxin subunit ArtA

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