SMTL ID : 1ydy.1

Crystal structure of periplasmic glycerophosphodiester phosphodiesterase from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.63, D.65, E.171 Ligands: GOL.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.63, A:D.65, A:E.171, H2O.1, H2O.6 CA.3: 4 residues within 4Å: Chain B: E.63, D.65, E.171 Ligands: GOL.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.63, B:D.65, B:E.171, H2O.15, H2O.21

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: H.36, E.63, E.171, Q.208, F.210, L.235, Y.313, F.344 Ligands: CA.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.36, A:Q.208, A:Q.208 Water bridges: A:R.37, A:R.37, A:K.173, A:K.173, A:K.173 GOL.4: 9 residues within 4Å: Chain B: H.36, E.63, E.171, Q.208, F.210, L.235, Y.313, F.344 Ligands: CA.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.36, B:Q.208, B:Q.208 Water bridges: B:R.37, B:K.173, B:K.173, B:T.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malashkevich, V.M. et al., Crystal structure of periplasmic glycerophosphodiester phosphodiesterase from Escherichia coli. To be Published

Release Date

2005-01-25

Peptides

Glycerophosphoryl diester phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycerophosphoryl diester phosphodiesterase