SMTL ID : 6fvk.1

Phosphotriesterase PTE_C23_3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 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, E8W.4 No protein-ligand interaction detected (PLIP) FMT.12: 10 residues within 4Å: Chain B: H.22, H.24, V.68, W.98, K.136, H.168, H.197 Ligands: ZN.13, ZN.14, E8W.15 No protein-ligand interaction detected (PLIP)

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, E8W.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, E8W.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.168, A:H.197 ZN.13: 7 residues within 4Å: Chain B: H.22, H.24, V.68, D.268 Ligands: FMT.12, ZN.14, E8W.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.22, B:H.24, B:D.268 ZN.14: 6 residues within 4Å: Chain B: W.98, H.168, H.197 Ligands: FMT.12, ZN.13, E8W.15 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.168, B:H.197

2 x E8W: 2-[methoxy(methyl)phosphoryl]oxypropane(Non-covalent)

E8W.4: 13 residues within 4Å: Chain A: H.22, H.24, I.73, W.98, H.168, H.197, D.268, L.270, F.273, S.275 Ligands: FMT.1, ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.73, A:W.98, A:L.270, A:F.273 E8W.15: 13 residues within 4Å: Chain B: H.22, H.24, I.73, W.98, H.168, H.197, D.268, L.270, F.273, S.275 Ligands: FMT.12, ZN.13, ZN.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.73, B:W.98, B:L.270, B:F.273

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain B: A.30, G.31, R.34, G.74, R.75, E.126 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.31, B:R.34, B:G.74, B:E.126 Water bridges: B:G.31, B:F.32, B:L.33, B:V.77 GOL.6: 6 residues within 4Å: Chain A: D.200, A.237, L.238, L.239, G.240, R.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.200, A:A.237, A:R.247 GOL.7: 3 residues within 4Å: Chain A: K.261, T.319, R.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.261, A:R.323 GOL.16: 6 residues within 4Å: Chain A: A.30, G.31, R.34, G.74, R.75, E.126 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.31, A:R.34, A:G.74, A:E.126 Water bridges: A:G.31, A:F.32, A:L.33, A:V.77 GOL.17: 6 residues within 4Å: Chain B: D.200, A.237, L.238, L.239, G.240, R.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.200, B:A.237, B:R.247 GOL.18: 3 residues within 4Å: Chain B: K.261, T.319, R.323 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.261, B:R.323

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

E8N.8: 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.19: 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 SO4: SULFATE ION(Non-functional Binders)

SO4.9: 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.203, A:R.242 SO4.10: 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 SO4.11: 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 Salt bridges: A:K.49, A:R.52, A:R.56 SO4.20: 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:R.242 SO4.21: 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 SO4.22: 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 Salt bridges: B:K.49, B:R.52, B:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dym, O. et al., PhosphotriesterasePTE_C23_3. To Be Published

Release Date

2019-03-20

Peptides

Parathion hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Parathion hydrolase

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