SMTL ID : 2ik2.1 (1 other biounit)

Yeast inorganic pyrophosphatase variant D115E with magnesium and phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.101, E.115, D.120, D.152 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.115, A:D.120, A:D.152, H2O.1, H2O.2, H2O.2 MG.2: 3 residues within 4Å: Chain A: Y.93, D.120 Ligands: PO4.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.120, H2O.2, H2O.2, H2O.2, H2O.2 MG.3: 3 residues within 4Å: Chain A: E.58 Ligands: PO4.5, PO4.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.58, H2O.5, H2O.10 MG.4: 6 residues within 4Å: Chain A: E.115, D.147, D.152, Y.192 Ligands: PO4.5, PO4.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.152, H2O.10 MG.7: 7 residues within 4Å: Chain B: E.115, D.120, D.152, K.154 Ligands: MG.8, MG.10, PO4.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.115, B:D.120, B:D.152, H2O.13, H2O.15 MG.8: 3 residues within 4Å: Chain B: D.120 Ligands: MG.7, PO4.11 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.120, H2O.12, H2O.12, H2O.12, H2O.13 MG.9: 4 residues within 4Å: Chain B: K.56, E.58 Ligands: PO4.11, PO4.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.58, H2O.22, H2O.23, H2O.26 MG.10: 7 residues within 4Å: Chain B: E.115, D.147, D.152, K.154 Ligands: MG.7, PO4.11, PO4.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.115, B:D.147, B:D.152, H2O.18

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

PO4.5: 8 residues within 4Å: Chain A: K.56, E.58, R.78, Y.192, K.193 Ligands: MG.3, MG.4, PO4.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.192 Water bridges: A:K.56, A:K.56, A:R.78, A:D.147, A:Y.192 Salt bridges: A:K.56, A:R.78, A:K.193 PO4.6: 10 residues within 4Å: Chain A: K.56, E.58, Y.93, D.120, D.152, K.154 Ligands: MG.2, MG.3, MG.4, PO4.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.93 Water bridges: A:D.117, A:D.152, A:D.152, A:K.154, A:K.154, A:K.154 Salt bridges: A:K.56, A:K.154 PO4.11: 14 residues within 4Å: Chain B: K.56, E.58, Y.93, E.115, D.117, D.120, D.147, D.152, K.154 Ligands: MG.7, MG.8, MG.9, MG.10, PO4.12 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.58, B:Y.93, B:E.115 Water bridges: B:E.48, B:K.56, B:K.154, B:K.154, B:Y.192 Salt bridges: B:K.56, B:K.154 PO4.12: 10 residues within 4Å: Chain B: K.56, E.58, R.78, E.115, D.147, Y.192, K.193 Ligands: MG.9, MG.10, PO4.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.192, B:Y.192, B:Y.192 Water bridges: B:K.56 Salt bridges: B:K.56, B:R.78, B:K.193

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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