SMTL ID : 2ik0.1

Yeast inorganic pyrophosphatase variant E48D with magnesium and phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: D.115, D.120, D.152 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.115, A:D.152, H2O.1, H2O.1, H2O.1 MG.2: 2 residues within 4Å: Chain A: R.78 Ligands: PO4.3 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: D.115, D.120, D.152, K.154 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.115, B:D.120, B:D.152, H2O.13, H2O.14, H2O.14 MG.5: 1 residues within 4Å: Ligands: PO4.6 No protein-ligand interaction detected (PLIP)

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 11 PLIP interactions: 11 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 Salt bridges: A:K.56, A:R.78, A:K.193 PO4.6: 6 residues within 4Å: Chain B: K.56, R.78, D.147, Y.192, K.193 Ligands: MG.5 17 PLIP interactions: 17 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:R.78, B:Y.93, B:D.147, B:D.147, B:D.147, B:K.193 Salt bridges: B:K.56, B:R.78, B:K.193

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 5 residues within 4Å: Chain B: L.182, R.183, N.186, S.206, G.207 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.183, B:N.186 Water bridges: B:A.209

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