SMTL ID : 3l12.1

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (YP_165505.1) from Silicibacter pomeroyi DSS-3 at 1.60 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.50, D.52, E.149 Ligands: UNL.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.50, A:D.52, A:E.149, H2O.1, H2O.2 MG.6: 4 residues within 4Å: Chain B: E.50, D.52, E.149 Ligands: UNL.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.50, B:D.52, B:E.149, H2O.15, H2O.17 MG.7: 1 residues within 4Å: Chain B: H.80 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.80

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: T.109, V.110 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: R.27 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: R.19, R.47 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: R.175, E.180, L.203 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: R.27, R.114 Ligand excluded by PLIP

2 x UNL: UNKNOWN LIGAND

UNL.5: 8 residues within 4Å: Chain A: H.23, E.50, E.149, H.186, F.188, L.208, W.274 Ligands: MG.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.186 Water bridges: A:R.24, A:R.24, A:R.24, A:R.24, A:E.149 UNL.10: 8 residues within 4Å: Chain B: H.23, E.50, E.149, H.186, F.188, L.208, W.274 Ligands: MG.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.23, B:H.186 Water bridges: B:R.24, B:R.24, B:R.24, B:R.24, B:R.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (YP_165505.1) from Silicibacter pomeroyi DSS-3 at 1.60 A resolution. To be published

Release Date

2009-12-29

Peptides

Putative Glycerophosphoryl diester phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative Glycerophosphoryl diester phosphodiesterase