This entry has been superseded by
8P7M
on Feb. 14, 2024, midnight.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FMT: FORMIC ACID(Non-functional Binders)
- 4 x ZN: ZINC ION(Non-covalent)
ZN.2: 7 residues within 4Å:- Chain A: H.29, H.31, V.75, D.275
- Ligands: FMT.1, ZN.3, GB.7
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:H.29, A:H.31, A:D.275
ZN.3: 6 residues within 4Å:- Chain A: W.105, H.175, H.204
- Ligands: FMT.1, ZN.2, GB.7
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:H.175, A:H.204
ZN.12: 7 residues within 4Å:- Chain B: H.29, H.31, V.75, D.275
- Ligands: FMT.11, ZN.13, GB.17
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:H.29, B:H.31, B:D.275
ZN.13: 6 residues within 4Å:- Chain B: W.105, H.175, H.204
- Ligands: FMT.11, ZN.12, GB.17
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:H.175, B:H.204
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 4 residues within 4Å:- Chain A: S.179, T.208, D.209, D.210
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:T.208, A:D.209, A:D.209, A:D.210
SO4.5: 3 residues within 4Å:- Chain A: W.251, Q.252, R.305
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.252
- Salt bridges: A:R.305
SO4.6: 2 residues within 4Å:- Chain A: S.196, P.197
2 PLIP interactions:2 interactions with chain A- Water bridges: A:L.195, A:S.198
SO4.14: 4 residues within 4Å:- Chain B: S.179, T.208, D.209, D.210
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:D.209, B:D.209, B:D.209, B:D.210
- Water bridges: B:D.210
SO4.15: 3 residues within 4Å:- Chain B: W.251, Q.252, R.305
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.252
- Salt bridges: B:R.305
SO4.16: 2 residues within 4Å:- Chain B: S.196, P.197
2 PLIP interactions:2 interactions with chain B- Water bridges: B:L.195, B:S.198
- 2 x GB: METHYLPHOSPHONIC ACID ESTER GROUP(Non-covalent)
GB.7: 10 residues within 4Å:- Chain A: H.29, H.31, W.105, E.106, H.175, H.204, D.275
- Ligands: FMT.1, ZN.2, ZN.3
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.106
GB.17: 10 residues within 4Å:- Chain B: H.29, H.31, W.105, E.106, H.175, H.204, D.275
- Ligands: FMT.11, ZN.12, ZN.13
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:H.31, B:H.175
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 7 residues within 4Å:- Chain A: Y.130, G.131, I.132, E.133, D.134, T.135, G.136
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:G.131, A:G.136
- Water bridges: A:R.126, A:D.134, A:T.135, A:T.135
GOL.9: 6 residues within 4Å:- Chain A: A.37, G.38, R.41, R.82, D.83, E.133
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:G.38, A:R.41, A:G.81, A:D.83
- Water bridges: A:F.39, A:L.40, A:V.84, A:V.84
GOL.10: 2 residues within 4Å:- Chain A: L.110, R.113
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.113
- Water bridges: A:R.113
GOL.18: 7 residues within 4Å:- Chain B: Y.130, G.131, I.132, E.133, D.134, T.135, G.136
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:G.131, B:G.136
- Water bridges: B:R.126, B:D.134, B:T.135, B:T.135
GOL.19: 6 residues within 4Å:- Chain B: A.37, G.38, R.41, R.82, D.83, E.133
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:G.38, B:R.41, B:G.81, B:D.83
- Water bridges: B:F.39, B:L.40, B:V.84, B:V.84
GOL.20: 2 residues within 4Å:- Chain B: L.110, R.113
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.113
- Water bridges: B:R.113
- 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
- 2019-03-13
- Peptides
- Parathion hydrolase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A