SMTL ID : 8p7k.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

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 10 residues within 4Å: Chain A: H.30, H.32, V.76, W.106, K.144, H.176, H.205 Ligands: ZN.2, ZN.3, E5N.4 No protein-ligand interaction detected (PLIP) FMT.5: 10 residues within 4Å: Chain B: H.30, H.32, V.76, W.106, K.144, H.176, H.205 Ligands: ZN.6, ZN.7, E5N.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.144

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: H.30, H.32, V.76, D.276 Ligands: FMT.1, ZN.3, E5N.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.30, A:H.32, A:D.276 ZN.3: 6 residues within 4Å: Chain A: W.106, H.176, H.205 Ligands: FMT.1, ZN.2, E5N.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.176, A:H.205 ZN.6: 6 residues within 4Å: Chain B: H.30, H.32, D.276 Ligands: FMT.5, ZN.7, E5N.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.30, B:H.32, B:D.276 ZN.7: 6 residues within 4Å: Chain B: W.106, H.176, H.205 Ligands: FMT.5, ZN.6, E5N.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.176, B:H.205

2 x E5N: (2~{R})-2-methylpentanedioic acid(Non-covalent)

E5N.4: 12 residues within 4Å: Chain A: H.30, H.32, W.106, H.176, H.205, H.232, L.246, D.276, F.281 Ligands: FMT.1, ZN.2, ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.106 Salt bridges: A:H.30, A:H.32, A:K.144, A:H.176, A:H.205 E5N.8: 12 residues within 4Å: Chain B: H.30, H.32, W.106, H.176, H.205, H.232, L.246, D.276, F.281 Ligands: FMT.5, ZN.6, ZN.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.106 Hydrogen bonds: B:D.276 Salt bridges: B:H.30, B:H.32, B:K.144, B:H.176, B:H.205, B:H.232

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

2023-06-07

Peptides

Parathion hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Parathion hydrolase

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