SMTL ID : 8uqz.1

Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gadolinium(III) Measured at 9.5 keV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 8 residues within 4Å: Chain A: F.19, I.301, R.305, Q.311, L.314, A.315, T.318, V.319 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.314, A:V.319 MPD.2: 13 residues within 4Å: Chain A: H.25, G.28, L.74, W.99, R.222, H.225, D.269, L.271, I.274, S.276, M.285 Ligands: GD3.3, CL.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.74, A:L.74, A:W.99, A:L.271, A:I.274 Hydrogen bonds: A:R.222 MPD.5: 8 residues within 4Å: Chain B: F.19, G.62, I.301, Q.311, L.314, A.315, T.318, V.319 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.301, B:V.319 MPD.7: 13 residues within 4Å: Chain B: H.25, G.28, L.74, W.99, R.222, H.225, F.239, D.269, L.271, I.274, S.276, M.285 Ligands: CL.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.74, B:L.74, B:W.99, B:L.271, B:I.274 Water bridges: B:D.269, B:D.269

1 x GD3: GADOLINIUM ION(Non-covalent)

GD3.3: 5 residues within 4Å: Chain A: H.23, H.25, D.269 Ligands: MPD.2, CL.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.23, A:H.25, A:D.269, A:D.269, H2O.5

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 9 residues within 4Å: Chain A: H.23, H.25, V.69, L.74, W.99, K.137, H.169 Ligands: MPD.2, GD3.3 Ligand excluded by PLIP CL.6: 8 residues within 4Å: Chain B: H.23, H.25, V.69, L.74, W.99, K.137, H.169 Ligands: MPD.7 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Breeze, C.W. et al., Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase. Acta Crystallogr D Struct Biol (2024)

Release Date

2024-04-03

Peptides

Phosphotriesterase variant PTE-R18: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphotriesterase variant PTE-R18

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