SMTL ID : 1t8q.1 (1 other biounit)

Structural genomics, Crystal structure of Glycerophosphoryl diester phosphodiesterase from E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.41, D.43, E.149 Ligands: GOL.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.41, A:D.43, A:E.149, H2O.1 MG.5: 4 residues within 4Å: Chain B: E.41, D.43, E.149 Ligands: GOL.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.41, B:D.43, B:E.149, H2O.14

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: H.14, R.15, E.41, D.43, E.149, K.151, F.188, Y.291, T.292 Ligands: MG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.15, A:K.151, A:K.151, A:T.292, A:T.292 GOL.3: 2 residues within 4Å: Chain A: K.173, Y.174 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.173 Water bridges: B:K.118, B:K.118 GOL.4: 3 residues within 4Å: Chain A: D.72, R.73, D.84 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.73 Water bridges: A:D.72, A:R.73, A:D.84 GOL.6: 9 residues within 4Å: Chain B: H.14, R.15, E.41, D.43, E.149, K.151, F.188, Y.291 Ligands: MG.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.14, B:R.15, B:K.151, B:K.151 Water bridges: B:Q.186 GOL.7: 3 residues within 4Å: Chain B: Q.134, K.173, Y.174 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.174 Hydrogen bonds: A:K.118 GOL.8: 3 residues within 4Å: Chain B: R.73, R.75, D.84 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.72, B:D.84 Water bridges: B:R.73, B:R.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, R. et al., The crystal structure of Glycerophosphoryl diester phosphodiesterase from E. coli. To be Published

Release Date

2004-08-03

Peptides

Glycerophosphoryl diester phosphodiesterase, periplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Glycerophosphoryl diester phosphodiesterase, periplasmic

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