SMTL ID : 1dpm.1

THREE-DIMENSIONAL STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTERASE WITH BOUND SUBSTRATE ANALOG DIETHYL 4-METHYLBENZYLPHOSPHONATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.21, H.23, D.267 Ligands: ZN.2, EBP.3, FMT.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.21, A:H.23, A:D.267, H2O.1 ZN.2: 6 residues within 4Å: Chain A: H.21, H.167, H.196 Ligands: ZN.1, EBP.3, FMT.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.167, A:H.196, H2O.1 ZN.6: 5 residues within 4Å: Chain B: H.21, H.23, D.267 Ligands: ZN.7, FMT.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.21, B:H.23, B:D.267, H2O.6 ZN.7: 6 residues within 4Å: Chain B: H.21, H.167, H.196 Ligands: ZN.6, EBP.8, FMT.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.167, B:H.196, H2O.6

4 x EBP: DIETHYL 4-METHYLBENZYLPHOSPHONATE(Non-covalent)

EBP.3: 11 residues within 4Å: Chain A: H.23, W.97, H.167, H.223, L.237, D.267, S.274, M.283 Ligands: ZN.1, ZN.2, FMT.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.237 pi-Cation interactions: A:H.220 EBP.4: 5 residues within 4Å: Chain A: L.117, R.118, Q.121, Y.122 Chain B: E.37 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.117, A:Y.122 pi-Stacking: A:Y.122 EBP.8: 10 residues within 4Å: Chain B: H.23, W.97, F.98, H.167, H.223, L.237, D.267, F.272, M.283 Ligands: ZN.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.237, B:L.237 EBP.9: 6 residues within 4Å: Chain A: E.37 Chain B: L.117, R.118, Q.121, Y.122, R.130 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.117, B:R.118, B:Y.122, B:Y.122

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

FMT.5: 11 residues within 4Å: Chain A: H.21, H.23, V.67, I.72, W.97, K.135, H.167, H.196 Ligands: ZN.1, ZN.2, EBP.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.67 FMT.10: 9 residues within 4Å: Chain B: H.21, H.23, V.67, W.97, K.135, H.167, H.196 Ligands: ZN.6, ZN.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanhooke, J.L. et al., Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate. Biochemistry (1996)

Release Date

1997-08-20

Peptides

PHOSPHOTRIESTERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PHOSPHOTRIESTERASE