SMTL ID : 2ihp.1

Yeast inorganic pyrophosphatase with magnesium and phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: D.115, D.120, D.152 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.115, A:D.120, A:D.152, H2O.1, H2O.1, H2O.1 MG.2: 1 residues within 4Å: Chain A: D.120 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.120, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.5: 5 residues within 4Å: Chain B: D.115, D.120, D.152, K.154 Ligands: MG.6 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.115, B:D.120, B:D.152, H2O.12, H2O.12, H2O.12 MG.6: 3 residues within 4Å: Chain B: D.117, D.120 Ligands: MG.5 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.120, H2O.12, H2O.12, H2O.12, H2O.12, H2O.12 MG.7: 1 residues within 4Å: Ligands: PO4.8 No protein-ligand interaction detected (PLIP)

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

PO4.3: 3 residues within 4Å: Chain A: K.73, R.78, K.198 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.193, A:K.198 Salt bridges: A:K.73, A:R.78, A:K.198 PO4.8: 6 residues within 4Å: Chain B: K.56, R.78, D.147, Y.192, K.193 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:D.147, B:Y.192, B:Y.192 Water bridges: B:K.56, B:K.56, B:K.56, B:K.56, B:R.78, B:Y.93, B:Y.93, B:D.147, B:D.147, B:D.147 Salt bridges: B:K.56, B:R.78, B:K.193

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 6 residues within 4Å: Chain A: T.60, K.61, E.62, I.69, D.71, T.72 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.60, A:K.61, A:E.62, A:T.72 Salt bridges: A:K.61, A:E.62, A:D.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oksanen, E. et al., A Complete Structural Description of the Catalytic Cycle of Yeast Pyrophosphatase. Biochemistry (2007)

Release Date

2007-02-13

Peptides

Inorganic pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Inorganic pyrophosphatase

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