SMTL ID : 3ks6.1 (3 other biounits)

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.80 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x UNL: UNKNOWN LIGAND

UNL.1: 8 residues within 4Å: Chain A: H.8, E.35, R.103, E.105, W.210, T.230 Ligands: MG.2, ACT.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.8, A:R.103, A:T.230 Water bridges: A:D.37, A:D.37, A:A.211

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.35, D.37, E.105 Ligands: UNL.1, ACT.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.35, A:D.37, A:E.105, H2O.1, H2O.2

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

CL.3: 4 residues within 4Å: Chain A: M.2, T.3, R.241, R.245 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 8 residues within 4Å: Chain A: H.8, R.9, H.50, F.140, W.210 Ligands: UNL.1, MG.2, ACT.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.140 Water bridges: A:R.9, A:D.37, A:H.50 Salt bridges: A:H.8, A:R.9, A:H.50 ACT.5: 2 residues within 4Å: Chain A: F.140 Ligands: ACT.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.140 Water bridges: A:E.105 Salt bridges: A:K.107

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

PEG.6: 5 residues within 4Å: Chain A: D.146, W.149, A.179, H.180, S.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.80 A resolution. To be published

Release Date

2009-12-08

Peptides

Glycerophosphoryl diester phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycerophosphoryl diester phosphodiesterase

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