SMTL ID : 7p85.1

Engineered phosphotriesterase BdPTE 10-2-C3(C59V/C227V) in complex with ethyl-4-methylbenzylphosphonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

2 x 5ZG: ethyl-4-methylbenzylphosphonate(Non-covalent)

5ZG.1: 17 residues within 4Å: Chain A: H.39, H.41, G.44, I.90, W.115, E.116, H.185, H.214, I.244, L.246, D.285, F.290, S.292 Chain B: L.120 Ligands: FMT.2, ZN.3, ZN.4 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.90, A:I.244, A:L.246, A:F.290, B:L.120 pi-Stacking: A:W.115 5ZG.11: 17 residues within 4Å: Chain A: L.120 Chain B: H.39, H.41, G.44, I.90, W.115, E.116, H.185, H.214, I.244, L.246, D.285, F.290, S.292 Ligands: FMT.12, ZN.13, ZN.14 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.90, B:I.244, B:L.246, B:F.290, A:L.120 pi-Stacking: B:W.115

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

FMT.2: 10 residues within 4Å: Chain A: H.39, H.41, V.85, W.115, K.153, H.185, H.214 Ligands: 5ZG.1, ZN.3, ZN.4 No protein-ligand interaction detected (PLIP) FMT.12: 10 residues within 4Å: Chain B: H.39, H.41, V.85, W.115, K.153, H.185, H.214 Ligands: 5ZG.11, ZN.13, ZN.14 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: H.39, H.41, D.285 Ligands: 5ZG.1, FMT.2, ZN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.39, A:H.41, A:D.285 ZN.4: 6 residues within 4Å: Chain A: W.115, H.185, H.214 Ligands: 5ZG.1, FMT.2, ZN.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.185, A:H.214 ZN.13: 6 residues within 4Å: Chain B: H.39, H.41, D.285 Ligands: 5ZG.11, FMT.12, ZN.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.39, B:H.41, B:D.285 ZN.14: 6 residues within 4Å: Chain B: W.115, H.185, H.214 Ligands: 5ZG.11, FMT.12, ZN.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.185, B:H.214

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

SO4.5: 3 residues within 4Å: Chain A: K.66, R.69, R.73 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.73, A:R.73, A:R.73 Salt bridges: A:K.66, A:R.69, A:R.73 SO4.6: 4 residues within 4Å: Chain A: R.123, T.161, P.162, F.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.163 Salt bridges: A:R.123 SO4.7: 3 residues within 4Å: Chain A: W.261, Q.262, R.315 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.261, A:Q.262 Salt bridges: A:R.315 SO4.15: 3 residues within 4Å: Chain B: K.66, R.69, R.73 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.73, B:R.73, B:R.73 Salt bridges: B:K.66, B:R.69, B:R.73 SO4.16: 4 residues within 4Å: Chain B: R.123, T.161, P.162, F.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.161, B:F.163 Salt bridges: B:R.123 SO4.17: 3 residues within 4Å: Chain B: W.261, Q.262, R.315 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.261, B:Q.262 Salt bridges: B:R.315

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: Y.140, G.141, I.142, E.143, D.144, T.145, G.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.141, A:G.146 Water bridges: A:T.145 GOL.9: 8 residues within 4Å: Chain A: A.47, G.48, R.51, G.91, R.92, D.93, E.143 Chain B: R.51 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.48, A:R.51, A:R.51, A:G.91, A:E.143 Water bridges: A:F.49, A:S.95, B:R.51 GOL.10: 3 residues within 4Å: Chain A: E.55 Chain B: Q.132, R.136 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.132, A:E.55 GOL.18: 7 residues within 4Å: Chain B: Y.140, G.141, I.142, E.143, D.144, T.145, G.146 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.141, B:G.146 Water bridges: B:Y.140, B:T.145 GOL.19: 8 residues within 4Å: Chain A: R.51 Chain B: A.47, G.48, R.51, G.91, R.92, D.93, E.143 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.48, B:R.51, B:R.51, B:G.91, B:E.143 Water bridges: B:F.49, B:S.95, A:R.51 GOL.20: 3 residues within 4Å: Chain A: Q.132, R.136 Chain B: E.55 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Job, L. et al., Structural and Functional Analysis of a Highly Active Designed Phosphotriesterase for the Detoxification of Organophosphate Nerve Agents Reveals an Unpredicted Conformation of the Active Site Loop. Biochemistry (2023)

Release Date

2022-08-03

Peptides

Parathion hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Parathion hydrolase