SMTL ID : 1e9g.1

STRUCTURE OF INORGANIC PYROPHOSPHATASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 8 residues within 4Å: Chain A: D.115, D.117, D.120, D.152, K.154 Ligands: MN.2, MN.4, 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.20, H2O.21 MN.2: 5 residues within 4Å: Chain A: Y.93, 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.20, H2O.20, H2O.20, H2O.21 MN.3: 5 residues within 4Å: Chain A: K.56, E.58, R.78 Ligands: PO4.5, PO4.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.58, H2O.20, H2O.20, H2O.20 MN.4: 8 residues within 4Å: Chain A: D.115, D.147, D.152, K.154, Y.192 Ligands: MN.1, PO4.5, PO4.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.147, A:D.152, H2O.20, H2O.20 MN.7: 8 residues within 4Å: Chain B: D.115, D.117, D.120, D.152, K.154 Ligands: MN.8, MN.10, PO4.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.115, B:D.120, B:D.152, H2O.39, H2O.39 MN.8: 4 residues within 4Å: Chain B: Y.93, D.120 Ligands: MN.7, PO4.12 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.120, H2O.39, H2O.39, H2O.39, H2O.40 MN.9: 5 residues within 4Å: Chain B: K.56, E.58, R.78 Ligands: PO4.11, PO4.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.58, H2O.40, H2O.40, H2O.40 MN.10: 8 residues within 4Å: Chain B: D.115, D.147, D.152, K.154, Y.192 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.40, H2O.40

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, A:Y.192, A:Y.192 Water bridges: A:K.73, A:K.73, A:R.78 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.120, D.152, K.154, Y.192 Ligands: MN.1, MN.2, MN.3, MN.4, PO4.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.93 Water bridges: A:K.154, A:K.154 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 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.192 Water bridges: B:K.56, B:R.78, B:K.193 Salt bridges: B:K.56, B:R.78, B:K.193 PO4.12: 13 residues within 4Å: Chain B: K.56, E.58, Y.93, D.115, D.120, D.152, K.154, Y.192 Ligands: MN.7, MN.8, MN.9, MN.10, PO4.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.93 Water bridges: B:K.154, B:K.154 Salt bridges: B:K.56, B:K.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heikinheimo, P. et al., Toward a Quantum-Mechanical Description of Metal-Assisted Phosphoryl Transfer in Pyrophosphatase. Proc.Natl.Acad.Sci.USA (2001)

Release Date

2001-03-19

Peptides

INORGANIC PYROPHOSPHATASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

INORGANIC PYROPHOSPHATASE

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