- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FMT: FORMIC ACID(Non-functional Binders)
- 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, 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.17: 6 residues within 4Å:- Chain B: H.22, H.24, D.268
- Ligands: FMT.16, ZN.18, VX.19
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:H.22, B:H.24, B:D.268
ZN.18: 6 residues within 4Å:- Chain B: W.98, H.168, H.197
- Ligands: FMT.16, ZN.17, VX.19
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:H.168, B:H.197
- 4 x VX: O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP(Non-covalent)
VX.4: 10 residues within 4Å:- Chain A: H.22, H.24, W.98, H.168, H.197, D.268, L.270
- Ligands: FMT.1, ZN.2, ZN.3
No protein-ligand interaction detected (PLIP)VX.12: 5 residues within 4Å:- Chain A: P.101, R.106, T.144, P.145, F.146
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:P.101
- Water bridges: A:F.146
VX.19: 10 residues within 4Å:- Chain B: H.22, H.24, W.98, H.168, H.197, D.268, L.270
- Ligands: FMT.16, ZN.17, ZN.18
No protein-ligand interaction detected (PLIP)VX.27: 5 residues within 4Å:- Chain B: P.101, R.106, T.144, P.145, F.146
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:P.101
- Hydrogen bonds: B:T.144
- Water bridges: B:F.146
- 2 x E8N: 1-ethyl-1-methyl-cyclohexane(Covalent)
E8N.5: 6 residues within 4Å:- Chain A: I.255, M.260, V.308, S.309, T.312
- Ligands: GOL.9
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:V.308, A:T.312
E8N.20: 6 residues within 4Å:- Chain B: I.255, M.260, V.308, S.309, T.312
- Ligands: GOL.24
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:V.308, B:T.312
- 12 x GOL: GLYCEROL(Non-functional Binders)
GOL.6: 8 residues within 4Å:- Chain A: Y.123, G.124, I.125, E.126, D.127, T.128, G.129
- Ligands: GOL.15
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:G.124, A:G.129
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:V.77, A:V.77
GOL.8: 5 residues within 4Å:- Chain A: W.98, E.99, S.275, Y.276
- Chain B: L.103
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.99, A:S.275
GOL.9: 5 residues within 4Å:- Chain A: K.252, D.256, K.306, G.307
- Ligands: E8N.5
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.252, A:K.252
GOL.10: 3 residues within 4Å:- Chain A: S.42, R.43, A.44
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.42, A:R.43, A:A.44
GOL.15: 2 residues within 4Å:- Chain A: Y.123
- Ligands: GOL.6
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.123, A:Y.123
GOL.21: 8 residues within 4Å:- Chain B: Y.123, G.124, I.125, E.126, D.127, T.128, G.129
- Ligands: GOL.30
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:G.124, B:G.129
- Water bridges: B:Y.123
GOL.22: 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:V.77, B:V.77
GOL.23: 5 residues within 4Å:- Chain A: L.103
- Chain B: W.98, E.99, S.275, Y.276
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.99, B:S.275
GOL.24: 5 residues within 4Å:- Chain B: K.252, D.256, K.306, G.307
- Ligands: E8N.20
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:K.252, B:K.252
GOL.25: 3 residues within 4Å:- Chain B: S.42, R.43, A.44
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.42, B:R.43, B:A.44
GOL.30: 2 residues within 4Å:- Chain B: Y.123
- Ligands: GOL.21
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Y.123
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.11: 2 residues within 4Å:- Chain A: W.244, Q.245
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:W.244, A:Q.245
SO4.13: 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.200, A:D.203
SO4.14: 3 residues within 4Å:- Chain A: K.261, T.319, R.323
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:K.261, A:R.323
SO4.26: 2 residues within 4Å:- Chain B: W.244, Q.245
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:W.244, B:Q.245
SO4.28: 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:D.200
SO4.29: 3 residues within 4Å:- Chain B: K.261, T.319, R.323
2 PLIP interactions:2 interactions with chain B- Salt bridges: B:K.261, B:R.323
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dym, O. et al., The impact of molecular variants, crystallization conditions and the space group on ligand-protein complexes: a case study on bacterial phosphotriesterase. Acta Crystallogr D Struct Biol (2023)
- Release Date
- 2023-10-25
- Peptides
- Parathion hydrolase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FMT: FORMIC ACID(Non-functional Binders)
- 4 x ZN: ZINC ION(Non-covalent)
- 4 x VX: O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP(Non-covalent)
- 2 x E8N: 1-ethyl-1-methyl-cyclohexane(Covalent)
- 12 x GOL: GLYCEROL(Non-functional Binders)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dym, O. et al., The impact of molecular variants, crystallization conditions and the space group on ligand-protein complexes: a case study on bacterial phosphotriesterase. Acta Crystallogr D Struct Biol (2023)
- Release Date
- 2023-10-25
- Peptides
- Parathion hydrolase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A