SMTL ID : 2qb7.2 (1 other biounit)

Saccharomyces cerevisiae cytosolic exopolyphosphatase, phosphate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: D.41, D.127, H.148, H.149 Ligands: PO4.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.41, A:D.127, A:D.127, A:H.148, H2O.12 CO.2: 3 residues within 4Å: Chain A: D.39 Ligands: PO4.3, PO4.4 No protein-ligand interaction detected (PLIP)

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 10 residues within 4Å: Chain A: N.35, S.37, D.39, D.127, H.148, H.149, K.268 Ligands: CO.1, CO.2, PO4.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.35, A:S.37, A:D.127 Water bridges: A:D.39, A:D.39, A:D.39, A:R.381 Salt bridges: A:H.149, A:K.268 PO4.4: 8 residues within 4Å: Chain A: H.149, K.268, T.380, R.381, K.382 Ligands: CO.2, PO4.3, PO4.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.381, A:K.382 Water bridges: A:H.149, A:K.268, A:K.268, A:R.381, A:K.382 Salt bridges: A:K.268, A:R.381 PO4.5: 5 residues within 4Å: Chain A: S.286, R.334, T.380, R.381 Ligands: PO4.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.286, A:R.381 Water bridges: A:R.334, A:R.334, A:T.380 Salt bridges: A:R.334, A:R.381

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

ACT.6: 3 residues within 4Å: Chain A: S.62, E.63, E.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.64 Water bridges: A:S.62 Salt bridges: A:K.66

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

EDO.7: 7 residues within 4Å: Chain A: H.148, H.149, F.150, D.151, V.163, K.164, V.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.151 Water bridges: A:H.148, A:F.150 EDO.8: 3 residues within 4Å: Chain A: K.289, R.290, W.326 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.290 EDO.9: 4 residues within 4Å: Chain A: H.148, S.166, G.167, K.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.167 Water bridges: A:S.166, A:K.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ugochukwu, E. et al., The crystal structure of the cytosolic exopolyphosphatase from Saccharomyces cerevisiae reveals the basis for substrate specificity. J.Mol.Biol. (2007)

Release Date

2007-12-11

Peptides

Exopolyphosphatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Exopolyphosphatase

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