SMTL ID : 3ks5.1 (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

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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

FE.1: 6 residues within 4Å: Chain A: E.35, D.37, E.105, K.107 Ligands: ACT.2, ACT.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.35, A:D.37, A:E.105, H2O.1

4 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.140 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.159, A:W.210 Water bridges: A:R.103, A:A.211 Salt bridges: A:H.8 ACT.4: 3 residues within 4Å: Chain A: P.162, S.163, Q.166 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.162, A:Q.166 ACT.5: 7 residues within 4Å: Chain A: M.197, Q.201, D.206, F.207, G.225, K.227 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.227 Hydrogen bonds: A:Q.201, A:F.207

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

EDO.6: 3 residues within 4Å: Chain A: S.161, P.162, S.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.161, A:S.163, A:S.163 EDO.7: 6 residues within 4Å: Chain A: R.9, D.17, H.49, H.50, D.51, T.57 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.9, A:H.49, A:H.50, A:D.51 Water bridges: A:D.17 EDO.8: 1 residues within 4Å: Chain A: E.175 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: L.168, G.169, G.171, A.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.172 Water bridges: A:G.171 EDO.10: 6 residues within 4Å: Chain A: G.1, M.2, T.3, G.225, V.226 Ligands: ACT.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.3, A:R.4

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
A

Glycerophosphoryl diester phosphodiesterase

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