SMTL ID : 2r1l.2 (1 other biounit)

OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x FE2: FE (II) ION(Non-covalent)

FE2.1: 6 residues within 4Å: Chain A: H.23, H.25, K.137, D.269 Ligands: CO.2, DPJ.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.23, A:H.25, A:D.269 FE2.5: 6 residues within 4Å: Chain B: H.23, H.25, K.137, D.269 Ligands: CO.6, DPJ.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.23, B:H.25, B:D.269

2 x CO: COBALT (II) ION(Non-covalent)

CO.2: 7 residues within 4Å: Chain A: W.99, K.137, H.169, H.198, R.222 Ligands: FE2.1, DPJ.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.169, A:H.198 CO.6: 7 residues within 4Å: Chain B: W.99, K.137, H.169, H.198, R.222 Ligands: FE2.5, DPJ.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.169, B:H.198

2 x DPJ: O,O-DIETHYL HYDROGEN THIOPHOSPHATE(Non-covalent)

DPJ.3: 17 residues within 4Å: Chain A: H.23, H.25, G.28, W.99, F.100, K.137, H.169, H.198, R.222, Y.225, L.239, D.269, L.271, F.274 Ligands: FE2.1, CO.2, EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.225, A:L.239, A:L.271, A:F.274 Hydrogen bonds: A:R.222 DPJ.7: 17 residues within 4Å: Chain B: H.23, H.25, G.28, W.99, F.100, K.137, H.169, H.198, R.222, Y.225, L.239, D.269, L.271, F.274 Ligands: FE2.5, CO.6, EDO.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.225, B:L.239, B:L.271, B:F.274 Hydrogen bonds: B:R.222

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: S.276, Y.277 Chain B: M.108 Ligands: DPJ.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.276 EDO.8: 4 residues within 4Å: Chain A: M.108 Chain B: S.276, Y.277 Ligands: DPJ.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jackson, C.J. et al., In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase. J.Mol.Biol. (2008)

Release Date

2008-02-12

Peptides

Phosphotriesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phosphotriesterase

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