SMTL ID : 2pz0.1

Crystal structure of Glycerophosphodiester Phosphodiesterase (GDPD) from T. tengcongensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.44, D.46, H.59, E.119 Ligands: GOL.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.44, A:D.46, A:E.119, H2O.1, H2O.5 CA.3: 4 residues within 4Å: Chain B: E.44, D.46, E.119 Ligands: GOL.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.44, B:D.46, B:E.119, H2O.5, H2O.9

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: H.17, E.44, E.119, F.152, L.172, W.217 Ligands: CA.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.44 Water bridges: A:R.18, A:R.18 GOL.4: 7 residues within 4Å: Chain B: H.17, E.44, E.119, F.152, L.172, W.217 Ligands: CA.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.17, B:E.44 Water bridges: B:R.18, B:R.18, B:R.18, B:E.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, L. et al., Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion-dependent enzyme: insight into the catalytic mechanism. Proteins (2008)

Release Date

2008-04-01

Peptides

Glycerophosphoryl diester phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycerophosphoryl diester phosphodiesterase