SMTL ID : 3ks5.2 (1 other biounit)

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: E.35, D.37, E.105 Ligands: ACT.2, ACT.3 6 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: A:E.35, A:D.37, A:E.105, H2O.1, ACT.2, ACT.3

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

ACT.2: 9 residues within 4Å: Chain A: H.8, R.9, D.37, H.50, E.105, K.107, F.140 Ligands: FE.1, ACT.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.140 Water bridges: A:H.8, A:K.107 Salt bridges: A:H.8, A:R.9, A:H.50, A:K.107 ACT.3: 9 residues within 4Å: Chain A: H.8, E.35, R.103, E.105, L.159, W.210, T.230 Ligands: FE.1, ACT.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.159, A:W.210 Water bridges: A:R.103, A:A.211, A:T.230 Salt bridges: A:H.8 ACT.4: 2 residues within 4Å: Chain A: Q.166, Q.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.167 Water bridges: A:Q.166, A:Q.166

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: L.168, G.169, P.170, G.171, A.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.169, A:G.171, A:A.172 EDO.6: 6 residues within 4Å: Chain A: R.9, D.17, H.50, D.51, A.56, T.57 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.17, A:H.50 Water bridges: A:D.17, A:H.50, A:D.51, A:D.51 EDO.7: 2 residues within 4Å: Chain A: T.242, R.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.245 Water bridges: A:T.242 EDO.8: 5 residues within 4Å: Chain A: P.114, Y.115, E.116, A.143, E.147 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.143 EDO.9: 3 residues within 4Å: Chain A: P.162, H.188, D.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.190

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 2.05 A resolution. To be published

Release Date

2009-12-08

Peptides

Glycerophosphoryl diester phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Glycerophosphoryl diester phosphodiesterase

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