SMTL ID : 6g0m.1

Phosphotriesterase PTE_C23_7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 10 residues within 4Å: Chain A: H.22, H.24, V.68, W.98, K.136, H.168, H.197 Ligands: ZN.2, ZN.3, VX.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.22 FMT.18: 10 residues within 4Å: Chain B: H.22, H.24, V.68, W.98, K.136, H.168, H.197 Ligands: ZN.19, ZN.20, VX.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.24

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: H.22, H.24, V.68, D.268 Ligands: FMT.1, ZN.3, VX.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.22, A:H.24, A:D.268 ZN.3: 6 residues within 4Å: Chain A: W.98, H.168, H.197 Ligands: FMT.1, ZN.2, VX.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.168, A:H.197 ZN.19: 7 residues within 4Å: Chain B: H.22, H.24, V.68, D.268 Ligands: FMT.18, ZN.20, VX.21 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.22, B:H.24, B:D.268 ZN.20: 6 residues within 4Å: Chain B: W.98, H.168, H.197 Ligands: FMT.18, ZN.19, VX.21 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.168, B:H.197

4 x VX: O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP(Non-covalent)

VX.4: 9 residues within 4Å: Chain A: H.22, H.24, W.98, H.168, H.197, D.268 Ligands: FMT.1, ZN.2, ZN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.197 VX.14: 6 residues within 4Å: Chain A: P.101, R.106, T.144, P.145, F.146, Q.147 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.101 Water bridges: A:F.146 VX.21: 9 residues within 4Å: Chain B: H.22, H.24, W.98, H.168, H.197, D.268 Ligands: FMT.18, ZN.19, ZN.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.197 VX.31: 6 residues within 4Å: Chain B: P.101, R.106, T.144, P.145, F.146, Q.147 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.101 Hydrogen bonds: B:T.144 Water bridges: B:F.146

2 x E8N: 1-ethyl-1-methyl-cyclohexane(Covalent)

E8N.5: 5 residues within 4Å: Chain A: I.255, V.308, S.309, T.312 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.255, A:V.308, A:T.312 E8N.22: 5 residues within 4Å: Chain B: I.255, V.308, S.309, T.312 Ligands: GOL.28 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.255, B:V.308, B:T.312

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: T.328, L.329, R.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.328, A:L.329, A:R.330 GOL.7: 7 residues within 4Å: Chain A: Y.123, G.124, I.125, E.126, D.127, T.128, G.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.124, A:G.129 GOL.8: 7 residues within 4Å: Chain A: A.30, G.31, R.34, G.74, R.75, D.76, E.126 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.31, A:R.34, A:R.34, A:G.74, A:E.126 Water bridges: A:F.32, A:L.33, A:V.77, A:V.77, A:S.78 GOL.9: 4 residues within 4Å: Chain A: W.98, E.99, S.275, Y.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.99, A:S.275 GOL.10: 5 residues within 4Å: Chain A: A.211, A.212, G.214, Y.259, Q.262 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain A: K.252, D.256, K.306, G.307 Ligands: E8N.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.252, A:D.256, A:K.306 GOL.12: 3 residues within 4Å: Chain A: S.42, R.43, A.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.42, A:R.43, A:A.44 GOL.23: 3 residues within 4Å: Chain B: T.328, L.329, R.330 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.329, B:R.330 GOL.24: 7 residues within 4Å: Chain B: Y.123, G.124, I.125, E.126, D.127, T.128, G.129 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.124, B:G.129 Water bridges: B:Y.123 GOL.25: 7 residues within 4Å: Chain B: A.30, G.31, R.34, G.74, R.75, D.76, E.126 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.31, B:R.34, B:R.34, B:G.74, B:E.126 Water bridges: B:F.32, B:L.33, B:V.77, B:V.77, B:S.78 GOL.26: 4 residues within 4Å: Chain B: W.98, E.99, S.275, Y.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.99, B:S.275 GOL.27: 5 residues within 4Å: Chain B: A.211, A.212, G.214, Y.259, Q.262 No protein-ligand interaction detected (PLIP) GOL.28: 5 residues within 4Å: Chain B: K.252, D.256, K.306, G.307 Ligands: E8N.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.252, B:D.256, B:K.306 GOL.29: 3 residues within 4Å: Chain B: S.42, R.43, A.44 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.42, B:R.43, B:A.44

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

SO4.13: 2 residues within 4Å: Chain A: W.244, Q.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.244, A:Q.245 SO4.15: 4 residues within 4Å: Chain A: S.172, T.201, D.202, D.203 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.202, A:D.203 Water bridges: A:S.172, A:D.200, A:T.201 SO4.16: 3 residues within 4Å: Chain A: K.49, R.52, R.56 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.49, A:R.56, A:P.289 Salt bridges: A:R.52, A:R.56 SO4.17: 3 residues within 4Å: Chain A: K.261, T.319, R.323 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.261, A:R.323 SO4.30: 2 residues within 4Å: Chain B: W.244, Q.245 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.244, B:Q.245 SO4.32: 4 residues within 4Å: Chain B: S.172, T.201, D.202, D.203 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.201, B:D.202, B:D.203 Water bridges: B:S.172, B:D.200 SO4.33: 3 residues within 4Å: Chain B: K.49, R.52, R.56 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.49, B:R.56, B:P.289 Salt bridges: B:R.52, B:R.56 SO4.34: 3 residues within 4Å: Chain B: K.261, T.319, R.323 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.261, B:R.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dym, O. et al., PhosphotriesterasePTE_C23_7. To Be Published

Release Date

2019-04-10

Peptides

Parathion hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Parathion hydrolase

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