SMTL ID : 3no3.1

Crystal structure of a glycerophosphodiester phosphodiesterase (BDI_0402) from Parabacteroides distasonis ATCC 8503 at 1.89 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.39, D.41, E.103 Ligands: GOL.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.39, A:D.41, A:E.103, H2O.1, H2O.1 MG.2: 1 residues within 4Å: Chain A: G.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.1, H2O.6

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: H.10, E.39, E.103, I.136, F.138, L.158, W.202, T.222 Ligands: MG.1 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.11, A:R.11, A:D.41, A:D.176, A:D.176, A:T.203

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: K.125, K.128, L.129, A.130, K.131 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.131 Hydrogen bonds: A:K.125, A:A.130, A:K.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a glycerophosphodiester phosphodiesterase (BDI_0402) from Parabacteroides distasonis ATCC 8503 at 1.89 A resolution. To be published

Release Date

2010-07-28

Peptides

glycerophosphodiester phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

glycerophosphodiester phosphodiesterase