SMTL ID : 6fef.1

Phosphotriesterase PTE_A53_2

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, IMD.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, IMD.14 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

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.12: 6 residues within 4Å: Chain B: H.22, H.24, D.268 Ligands: FMT.11, ZN.13, IMD.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.22, B:H.24, B:D.268, H2O.11 ZN.13: 6 residues within 4Å: Chain B: W.98, H.168, H.197 Ligands: FMT.11, ZN.12, IMD.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.168, B:H.197, H2O.11, H2O.11

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 7 residues within 4Å: Chain A: H.24, W.98, D.268, F.273 Ligands: FMT.1, ZN.2, ZN.3 No protein-ligand interaction detected (PLIP) IMD.14: 7 residues within 4Å: Chain B: H.24, W.98, D.268, F.273 Ligands: FMT.11, ZN.12, ZN.13 No protein-ligand interaction detected (PLIP)

6 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.123, A:G.124, A:G.129 Water bridges: A:R.119, A:D.127, A:T.128, A:T.128 GOL.6: 6 residues within 4Å: Chain A: A.30, G.31, R.34, R.75, D.76, E.126 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.31, A:R.34, A:R.75, A:D.76 Water bridges: A:F.32, A:L.33, A:V.77, A:V.77 GOL.7: 1 residues within 4Å: Chain A: Y.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.123 GOL.15: 7 residues within 4Å: Chain B: Y.123, G.124, I.125, E.126, D.127, T.128, G.129 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.123, B:G.124, B:G.129 Water bridges: B:R.119, B:D.127, B:T.128, B:T.128 GOL.16: 6 residues within 4Å: Chain B: A.30, G.31, R.34, R.75, D.76, E.126 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.31, B:R.34, B:R.75, B:D.76 Water bridges: B:F.32, B:L.33, B:D.76, B:V.77 GOL.17: 1 residues within 4Å: Chain B: Y.123 No protein-ligand interaction detected (PLIP)

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

SO4.8: 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 SO4.9: 4 residues within 4Å: Chain A: S.172, T.201, D.202, D.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.201, A:D.202, A:D.202, A:D.203 SO4.10: 3 residues within 4Å: Chain A: K.49, R.52, R.56 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.49, A:R.56 Salt bridges: A:R.52, A:R.56 SO4.18: 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 SO4.19: 4 residues within 4Å: Chain B: S.172, T.201, D.202, D.203 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.201, B:T.201, B:D.202, B:D.203 SO4.20: 3 residues within 4Å: Chain B: K.49, R.52, R.56 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.49, B:R.56 Salt bridges: B:R.52, B:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dym, O. et al., Crystal Structures of Bacterial Phosphotriesterase Variants with High Catalytic Activity Towards Organophosphate Nerve Agents Developed by Use of Structure-Based Design and Molecular Evolution. To Be Published

Release Date

2019-01-30

Peptides

Phosphotriesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phosphotriesterase

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