- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.77 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, X3B.8
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, X3B.8
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:H.168, A:H.197
ZN.11: 6 residues within 4Å:- Chain B: H.22, H.24, D.268
- Ligands: FMT.10, ZN.12, X3B.17
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:H.22, B:H.24, B:D.268
ZN.12: 6 residues within 4Å:- Chain B: W.98, H.168, H.197
- Ligands: FMT.10, ZN.11, X3B.17
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:H.168, B:H.197
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 7 residues within 4Å:- Chain A: Y.123, G.124, I.125, E.126, D.127, T.128, G.129
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Y.123, A:G.124, A:G.129
- Water bridges: A:T.128
GOL.5: 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.6: 1 residues within 4Å:- Chain A: Y.123
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.123
GOL.13: 7 residues within 4Å:- Chain B: Y.123, G.124, I.125, E.126, D.127, T.128, G.129
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Y.123, B:G.124, B:G.129
- Water bridges: B:T.128
GOL.14: 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.15: 1 residues within 4Å:- Chain B: Y.123
No protein-ligand interaction detected (PLIP)- 2 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 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
SO4.16: 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
- 2 x X3B: 2-methylidene-1,3-dioxane-4,4-diol(Non-covalent)
X3B.8: 12 residues within 4Å:- Chain A: H.22, H.24, W.98, H.168, H.197, H.224, D.268, L.270, F.273
- Ligands: FMT.1, ZN.2, ZN.3
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:W.98
- Salt bridges: A:H.24
X3B.17: 12 residues within 4Å:- Chain B: H.22, H.24, W.98, H.168, H.197, H.224, D.268, L.270, F.273
- Ligands: FMT.10, ZN.11, ZN.12
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:W.98
- Hydrogen bonds: B:W.98, B:D.268
- Salt bridges: B:H.24
- 2 x EDO: 1,2-ETHANEDIOL(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
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.77 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FMT: FORMIC ACID(Non-functional Binders)
- 4 x ZN: ZINC ION(Non-covalent)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- 2 x SO4: SULFATE ION(Non-functional Binders)
- 2 x X3B: 2-methylidene-1,3-dioxane-4,4-diol(Non-covalent)
- 2 x EDO: 1,2-ETHANEDIOL(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