SMTL ID : 1ypp.1

ACID ANHYDRIDE HYDROLASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.115, D.120, D.152 Ligands: MN.2, MN.3, PO4.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.115, A:D.120, A:D.152, H2O.1, H2O.1 MN.2: 4 residues within 4Å: Chain A: D.117, D.120 Ligands: MN.1, PO4.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.120, H2O.1, H2O.3, H2O.3, H2O.3 MN.3: 6 residues within 4Å: Chain A: D.115, D.147, D.152 Ligands: MN.1, PO4.5, PO4.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.147, A:D.152, H2O.1 MN.4: 4 residues within 4Å: Chain A: K.56, 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.1, H2O.1 MN.7: 6 residues within 4Å: Chain B: D.115, D.120, D.152 Ligands: MN.8, MN.9, PO4.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.115, B:D.120, B:D.152 MN.8: 3 residues within 4Å: Chain B: D.120 Ligands: MN.7, PO4.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.120, H2O.7 MN.9: 5 residues within 4Å: Chain B: D.147, D.152 Ligands: MN.7, PO4.11, PO4.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.147, B:D.152, H2O.5, H2O.6 MN.10: 4 residues within 4Å: Chain B: K.56, E.58 Ligands: PO4.11, PO4.12 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, H2O.5, H2O.6

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

PO4.5: 9 residues within 4Å: Chain A: K.56, E.58, R.78, D.147, Y.192, K.193 Ligands: MN.3, MN.4, PO4.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.192 Water bridges: A:K.56, A:R.78, A:R.78, A:K.193, A:K.193 Salt bridges: A:K.56, A:R.78, A:K.193 PO4.6: 13 residues within 4Å: Chain A: K.56, E.58, Y.93, D.115, D.117, D.120, D.152, K.154 Ligands: MN.1, MN.2, MN.3, MN.4, PO4.5 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.56, A:K.154 PO4.11: 9 residues within 4Å: Chain B: K.56, E.58, R.78, D.147, Y.192, K.193 Ligands: MN.9, MN.10, PO4.12 11 PLIP interactions: 11 interactions with chain B Water bridges: B:K.56, B:R.78, B:D.115, B:E.148, B:E.148, B:E.148, B:Y.192, B:Y.192 Salt bridges: B:K.56, B:R.78, B:K.193 PO4.12: 12 residues within 4Å: Chain B: K.56, E.58, Y.93, D.115, D.120, D.152, K.154 Ligands: MN.7, MN.8, MN.9, MN.10, PO4.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.115 Water bridges: B:K.56, B:K.56, B:K.56, B:Y.93, B:Y.192 Salt bridges: B:K.56, B:K.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harutyunyan, E.H. et al., X-ray structure of yeast inorganic pyrophosphatase complexed with manganese and phosphate. Eur.J.Biochem. (1996)

Release Date

1996-12-07

Peptides

INORGANIC PYROPHOSPHATASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INORGANIC PYROPHOSPHATASE