SMTL ID : 2ik7.1

Yeast inorganic pyrophosphatase variant D120N with magnesium and phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.115, N.120, D.152 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.115, A:D.152, H2O.2, H2O.4, H2O.4 MG.2: 3 residues within 4Å: Chain A: E.58, R.78 Ligands: PO4.3 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: D.115, N.120, D.152, K.154 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.115, B:D.152, H2O.14, H2O.14, H2O.15

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

PO4.3: 6 residues within 4Å: Chain A: K.56, R.78, D.147, Y.192, K.193 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.147, A:Y.192, A:Y.192 Water bridges: A:K.56, A:K.56, A:K.56, A:K.56, A:R.78, A:D.115, A:D.115, A:D.115, A:D.117, A:N.120, A:K.193, A:K.193 Salt bridges: A:K.56, A:R.78, A:K.193 PO4.5: 5 residues within 4Å: Chain B: K.56, R.78, D.147, Y.192, K.193 20 PLIP interactions: 20 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:K.56, B:D.71, B:R.78, B:R.78, B:Y.93, B:Y.93, B:N.120, B:D.147, B:D.147, B:D.147 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