SMTL ID : 6g1j.1

Phosphotriesterase PTE_C23M_1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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, IMD.4 No protein-ligand interaction detected (PLIP) FMT.15: 10 residues within 4Å: Chain B: H.22, H.24, V.68, W.98, K.136, H.168, H.197 Ligands: ZN.16, ZN.17, IMD.18 No protein-ligand interaction detected (PLIP)

8 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 6 residues within 4Å: Chain A: H.22, H.24, D.268 Ligands: FMT.1, ZN.3, IMD.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.22, A:H.24, A:D.268, H2O.1 ZN.3: 6 residues within 4Å: Chain A: W.98, H.168, H.197 Ligands: FMT.1, ZN.2, IMD.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.168, A:H.197, H2O.1, H2O.1 ZN.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.12: 2 residues within 4Å: Chain A: D.200, R.247 No protein-ligand interaction detected (PLIP) ZN.16: 6 residues within 4Å: Chain B: H.22, H.24, D.268 Ligands: FMT.15, ZN.17, IMD.18 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.22, B:H.24, B:D.268, H2O.7 ZN.17: 6 residues within 4Å: Chain B: W.98, H.168, H.197 Ligands: FMT.15, ZN.16, IMD.18 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.168, B:H.197, H2O.7, H2O.7 ZN.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.26: 2 residues within 4Å: Chain B: D.200, R.247 No protein-ligand interaction detected (PLIP)

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 5 residues within 4Å: Chain A: H.24, D.268 Ligands: FMT.1, ZN.2, ZN.3 No protein-ligand interaction detected (PLIP) IMD.18: 5 residues within 4Å: Chain B: H.24, D.268 Ligands: FMT.15, ZN.16, ZN.17 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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.6: 7 residues within 4Å: Chain A: A.30, G.31, R.34, G.74, R.75, D.76, E.126 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.31, A:R.34, A:R.34, A:G.74, A:D.76 Water bridges: A:F.32, A:V.77, A:V.77 GOL.7: 4 residues within 4Å: Chain A: R.106, T.144, P.145, F.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.106, A:F.146 Water bridges: A:Q.147 GOL.8: 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.19: 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.20: 7 residues within 4Å: Chain B: A.30, G.31, R.34, G.74, R.75, D.76, E.126 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.31, B:R.34, B:R.34, B:G.74, B:D.76 Water bridges: B:F.32, B:V.77, B:V.77 GOL.21: 4 residues within 4Å: Chain B: R.106, T.144, P.145, F.146 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.106, B:T.144, B:F.146 Water bridges: B:Q.147 GOL.22: 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

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

SO4.9: 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 SO4.10: 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 SO4.14: 3 residues within 4Å: Chain A: K.49, R.52, R.56 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.53 Salt bridges: A:K.49, A:R.52, A:R.56 SO4.23: 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 SO4.24: 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 SO4.28: 3 residues within 4Å: Chain B: K.49, R.52, R.56 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.53 Salt bridges: B:K.49, B:R.52, B:R.56

2 x E8N: 1-ethyl-1-methyl-cyclohexane(Non-covalent)

E8N.13: 4 residues within 4Å: Chain A: I.255, V.308, S.309, T.312 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.255, A:V.308, A:T.312 E8N.27: 4 residues within 4Å: Chain B: I.255, V.308, S.309, T.312 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.255, B:V.308, B:T.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dym, O. et al., PhosphotriesterasePTE_C23M_1. 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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