SMTL ID : 8p7h.1

The impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes

Coordinates

PDB Format Compare

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, X3B.8 No protein-ligand interaction detected (PLIP) FMT.10: 10 residues within 4Å: Chain B: H.22, H.24, V.68, W.98, K.136, H.168, H.197 Ligands: ZN.11, ZN.12, X3B.17 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, 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)

EDO.9: 5 residues within 4Å: Chain A: W.98, E.99, S.275, Y.276 Chain B: L.103 No protein-ligand interaction detected (PLIP) EDO.18: 5 residues within 4Å: Chain A: L.103 Chain B: W.98, E.99, S.275, Y.276 No protein-ligand interaction detected (PLIP)

Links

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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
A

B
A

Parathion hydrolase