SMTL ID : 6g3m.1

Phosphotriesterase PTE_C23M_4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 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 No protein-ligand interaction detected (PLIP) FMT.11: 10 residues within 4Å: Chain B: H.22, H.24, V.68, W.98, K.136, H.168, H.197 Ligands: ZN.12, ZN.13, VX.14 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 8 residues within 4Å: Chain A: H.22, H.24, V.68, K.136, 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.12: 8 residues within 4Å: Chain B: H.22, H.24, V.68, K.136, D.268 Ligands: FMT.11, ZN.13, VX.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.22, B:H.24, B:D.268 ZN.13: 6 residues within 4Å: Chain B: W.98, H.168, H.197 Ligands: FMT.11, ZN.12, VX.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.168, B:H.197

2 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 No protein-ligand interaction detected (PLIP) VX.14: 9 residues within 4Å: Chain B: H.22, H.24, W.98, H.168, H.197, D.268 Ligands: FMT.11, ZN.12, ZN.13 No protein-ligand interaction detected (PLIP)

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

E8N.5: 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.15: 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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: Y.123, G.124, I.125, E.126, D.127, T.128, G.129 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.124, A:G.129 Water bridges: A:R.119, A:R.119, A:T.128 GOL.7: 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:E.126 Water bridges: A:F.32, A:L.33, A:V.77 GOL.8: 5 residues within 4Å: Chain A: R.106, T.144, P.145, F.146, Q.147 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.106, A:T.144, A:T.144, A:F.146 Water bridges: A:Q.147 GOL.16: 7 residues within 4Å: Chain B: Y.123, G.124, I.125, E.126, D.127, T.128, G.129 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.124, B:G.129 Water bridges: B:R.119, B:R.119, B:T.128 GOL.17: 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:E.126 Water bridges: B:F.32, B:L.33, B:V.77 GOL.18: 5 residues within 4Å: Chain B: R.106, T.144, P.145, F.146, Q.147 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.106, B:T.144, B:T.144, B:F.146 Water bridges: B:Q.147

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

SO4.9: 3 residues within 4Å: Chain A: W.244, Q.245, R.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.244, A:Q.245 Salt bridges: A:R.298 SO4.19: 3 residues within 4Å: Chain B: W.244, Q.245, R.298 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.244, B:Q.245 Salt bridges: B:R.298

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 2 residues within 4Å: Chain A: W.244, R.298 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: W.244, R.298 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dym, O. et al., PhosphotriesterasePTE_C23M_4. 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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