SMTL ID : 1e6a.1

Fluoride-inhibited substrate complex of Saccharomyces cerevisiae inorganic pyrophosphatase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.120, D.152 Ligands: MN.2, MN.4, POP.5, F.6, NA.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.115, A:D.120, A:D.152, H2O.13 MN.2: 4 residues within 4Å: Chain A: D.120 Ligands: MN.1, POP.5, F.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.120, H2O.13, H2O.13, H2O.13 MN.3: 3 residues within 4Å: Chain A: E.58 Ligands: POP.5, NA.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.58, H2O.13, H2O.14, H2O.14 MN.4: 6 residues within 4Å: Chain A: D.115, D.147, D.152, Y.192 Ligands: MN.1, POP.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.147, A:D.152, H2O.14, H2O.14 MN.8: 8 residues within 4Å: Chain B: D.115, D.120, D.152 Ligands: MN.9, MN.11, POP.12, PO4.14, F.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.115, B:D.120, B:D.152, H2O.25 MN.9: 5 residues within 4Å: Chain B: D.120 Ligands: MN.8, POP.12, PO4.14, F.15 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.120, H2O.25, H2O.25, H2O.25 MN.10: 6 residues within 4Å: Chain B: K.56, E.58, D.117 Ligands: POP.12, PO4.13, PO4.14 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.58, H2O.25, H2O.25, H2O.25 MN.11: 8 residues within 4Å: Chain B: D.115, D.147, D.152, Y.192 Ligands: MN.8, POP.12, PO4.13, PO4.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.147, B:D.152, H2O.25, H2O.25

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.5: 17 residues within 4Å: Chain A: K.56, E.58, R.78, Y.93, D.115, D.117, D.120, D.147, D.152, Y.192, K.193 Ligands: MN.1, MN.2, MN.3, MN.4, F.6, NA.7 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.93, A:Y.192 Water bridges: A:K.56, A:K.56, A:K.154, A:K.193, A:K.193 Salt bridges: A:K.56, A:K.56, A:R.78, A:K.154, A:K.193 POP.12: 18 residues within 4Å: Chain B: K.56, E.58, R.78, Y.93, D.115, D.117, D.120, D.147, D.152, Y.192, K.193 Ligands: MN.8, MN.9, MN.10, MN.11, PO4.13, PO4.14, F.15 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:E.58, B:D.115, B:D.117, B:Y.192 Water bridges: B:R.78, B:Y.89, B:Y.93, B:Y.93, B:K.193, B:K.193 Salt bridges: B:K.56, B:K.56, B:R.78, B:K.154, B:K.193

2 x F: FLUORIDE ION(Non-covalent)

F.6: 7 residues within 4Å: Chain A: D.115, D.117, D.120 Ligands: MN.1, MN.2, POP.5, NA.7 No protein-ligand interaction detected (PLIP) F.15: 7 residues within 4Å: Chain B: D.115, D.117, D.120 Ligands: MN.8, MN.9, POP.12, PO4.14 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain A: D.115, D.117 Ligands: MN.1, MN.3, POP.5, F.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.115

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

PO4.13: 10 residues within 4Å: Chain B: K.56, E.58, R.78, D.147, Y.192, K.193 Ligands: MN.10, MN.11, POP.12, PO4.14 8 PLIP interactions: 8 interactions with chain B Water bridges: B:K.56, B:R.78, B:K.193, B:K.193, B:K.193 Salt bridges: B:K.56, B:R.78, B:K.193 PO4.14: 14 residues within 4Å: Chain B: K.56, E.58, Y.93, D.115, D.117, D.120, D.152 Ligands: MN.8, MN.9, MN.10, MN.11, POP.12, PO4.13, F.15 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.58, B:D.115, B:D.117 Water bridges: B:Y.93, B:Y.93 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. U.S.A. (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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