SMTL ID : 3q46.1

Magnesium activated Inorganic pyrophosphatase from Thermococcus thioreducens bound to hydrolyzed product at 0.99 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.99 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 12 residues within 4Å: Chain A: K.30, E.32, Y.56, D.66, D.71, D.103, K.105 Ligands: MG.2, MG.3, MG.4, MG.5, CL.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.71 Water bridges: A:K.30, A:K.30, A:K.105, A:K.105 Salt bridges: A:K.30, A:K.105 PO4.8: 12 residues within 4Å: Chain B: K.30, E.32, Y.56, D.66, D.71, D.103, K.105 Ligands: MG.9, MG.10, MG.11, MG.12, CL.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.71 Water bridges: B:K.30, B:K.30, B:K.105, B:K.105 Salt bridges: B:K.30, B:K.105 PO4.15: 12 residues within 4Å: Chain C: K.30, E.32, Y.56, D.66, D.71, D.103, K.105 Ligands: MG.16, MG.17, MG.18, MG.19, CL.21 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.71, C:D.98, C:D.98 Water bridges: C:K.30, C:K.30, C:D.71, C:K.105 Salt bridges: C:K.30, C:K.105 PO4.22: 12 residues within 4Å: Chain D: K.30, E.32, Y.56, D.66, D.71, D.103, K.105 Ligands: MG.23, MG.24, MG.25, MG.26, CL.28 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:E.32, D:Y.56, D:D.71 Water bridges: D:K.30, D:K.30, D:D.66, D:D.66, D:D.68, D:K.105, D:K.105 Salt bridges: D:K.30, D:K.105 PO4.29: 12 residues within 4Å: Chain E: K.30, E.32, Y.56, D.66, D.71, D.103, K.105 Ligands: MG.30, MG.31, MG.32, MG.33, CL.35 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:E.32, E:Y.56, E:D.71, E:D.98 Water bridges: E:K.30, E:K.30, E:D.66, E:D.66, E:D.68, E:K.105 Salt bridges: E:K.30, E:K.105 PO4.36: 12 residues within 4Å: Chain F: K.30, E.32, Y.56, D.66, D.71, D.103, K.105 Ligands: MG.37, MG.38, MG.39, MG.40, CL.42 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:E.32, F:Y.56, F:D.71 Water bridges: F:K.30, F:K.30, F:D.66, F:D.66, F:D.68, F:K.105, F:K.105 Salt bridges: F:K.30, F:K.105

24 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.71 Ligands: PO4.1, MG.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.71, H2O.1, H2O.1, H2O.11 MG.3: 7 residues within 4Å: Chain A: D.66, D.71, D.103, K.105 Ligands: PO4.1, MG.2, MG.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.66, A:D.71, A:D.103, H2O.11 MG.4: 6 residues within 4Å: Chain A: D.66, D.98, D.103, K.105 Ligands: PO4.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.98, A:D.103, H2O.2, H2O.2, H2O.2 MG.5: 2 residues within 4Å: Chain A: E.32 Ligands: PO4.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.32, H2O.3, H2O.11, H2O.11, H2O.11 MG.9: 3 residues within 4Å: Chain B: D.71 Ligands: PO4.8, MG.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.71, H2O.12, H2O.12, H2O.23 MG.10: 7 residues within 4Å: Chain B: D.66, D.71, D.103, K.105 Ligands: PO4.8, MG.9, MG.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.66, B:D.71, B:D.103, H2O.22 MG.11: 6 residues within 4Å: Chain B: D.66, D.98, D.103, K.105 Ligands: PO4.8, MG.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.103, H2O.13, H2O.13, H2O.13 MG.12: 2 residues within 4Å: Chain B: E.32 Ligands: PO4.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.32, H2O.14, H2O.22, H2O.22, H2O.22 MG.16: 3 residues within 4Å: Chain C: D.71 Ligands: PO4.15, MG.17 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.71, H2O.23, H2O.23, H2O.34 MG.17: 7 residues within 4Å: Chain C: D.66, D.71, D.103, K.105 Ligands: PO4.15, MG.16, MG.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.66, C:D.71, C:D.103, H2O.34 MG.18: 6 residues within 4Å: Chain C: D.66, D.98, D.103, K.105 Ligands: PO4.15, MG.17 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.98, C:D.103, H2O.24, H2O.25, H2O.25 MG.19: 2 residues within 4Å: Chain C: E.32 Ligands: PO4.15 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.32, H2O.25, H2O.34, H2O.34, H2O.34 MG.23: 3 residues within 4Å: Chain D: D.71 Ligands: PO4.22, MG.24 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.71, H2O.35, H2O.35, H2O.45 MG.24: 7 residues within 4Å: Chain D: D.66, D.71, D.103, K.105 Ligands: PO4.22, MG.23, MG.25 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.66, D:D.71, D:D.103, H2O.45 MG.25: 6 residues within 4Å: Chain D: D.66, D.98, D.103, K.105 Ligands: PO4.22, MG.24 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.98, D:D.103, H2O.36, H2O.36, H2O.36 MG.26: 2 residues within 4Å: Chain D: E.32 Ligands: PO4.22 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.32, H2O.37, H2O.45, H2O.45, H2O.45 MG.30: 3 residues within 4Å: Chain E: D.71 Ligands: PO4.29, MG.31 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.71, H2O.46, H2O.46, H2O.57 MG.31: 7 residues within 4Å: Chain E: D.66, D.71, D.103, K.105 Ligands: PO4.29, MG.30, MG.32 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.66, E:D.71, E:D.103, H2O.56 MG.32: 6 residues within 4Å: Chain E: D.66, D.98, D.103, K.105 Ligands: PO4.29, MG.31 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.98, E:D.103, H2O.47, H2O.47, H2O.47 MG.33: 2 residues within 4Å: Chain E: E.32 Ligands: PO4.29 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:E.32, H2O.48, H2O.56, H2O.56, H2O.56 MG.37: 3 residues within 4Å: Chain F: D.71 Ligands: PO4.36, MG.38 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.71, H2O.57, H2O.57, H2O.68 MG.38: 7 residues within 4Å: Chain F: D.66, D.71, D.103, K.105 Ligands: PO4.36, MG.37, MG.39 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.66, F:D.71, F:D.103, H2O.68 MG.39: 6 residues within 4Å: Chain F: D.66, D.98, D.103, K.105 Ligands: PO4.36, MG.38 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.98, F:D.103, H2O.58, H2O.59, H2O.59 MG.40: 2 residues within 4Å: Chain F: E.32 Ligands: PO4.36 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.32, H2O.59, H2O.68, H2O.68, H2O.68

6 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 8 residues within 4Å: Chain A: D.65, D.66, G.67, D.98, S.99, D.101, K.141, K.146 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.65, A:D.98 Water bridges: A:K.141, A:K.146, A:K.146 Salt bridges: A:R.44, A:D.101, A:D.101, A:K.141, A:K.146 EPE.13: 8 residues within 4Å: Chain B: D.65, D.66, G.67, D.98, S.99, D.101, K.141, K.146 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.65, B:D.98 Water bridges: B:K.141, B:K.146, B:K.146 Salt bridges: B:R.44, B:D.101, B:D.101, B:K.141, B:K.146 EPE.20: 8 residues within 4Å: Chain C: D.65, D.66, G.67, D.98, S.99, D.101, K.141, K.146 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:D.65, C:D.98 Water bridges: C:K.141, C:K.146, C:K.146 Salt bridges: C:R.44, C:D.101, C:D.101, C:K.141, C:K.146 EPE.27: 8 residues within 4Å: Chain D: D.65, D.66, G.67, D.98, S.99, D.101, K.141, K.146 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:D.65, D:D.98 Water bridges: D:D.101, D:K.141, D:K.146, D:K.146 Salt bridges: D:R.44, D:D.101, D:D.101, D:K.141, D:K.146 EPE.34: 8 residues within 4Å: Chain E: D.65, D.66, G.67, D.98, S.99, D.101, K.141, K.146 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:D.65, E:D.98 Water bridges: E:D.101, E:K.141, E:K.146, E:K.146 Salt bridges: E:R.44, E:D.101, E:D.101, E:K.141, E:K.146 EPE.41: 8 residues within 4Å: Chain F: D.65, D.66, G.67, D.98, S.99, D.101, K.141, K.146 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:D.65, F:D.98 Water bridges: F:D.101, F:K.141, F:K.146, F:K.146 Salt bridges: F:R.44, F:D.101, F:D.101, F:K.141, F:K.146

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 6 residues within 4Å: Chain A: K.30, Y.52, Y.56, F.137, Y.140 Ligands: PO4.1 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain B: K.30, Y.52, Y.56, F.137, Y.140 Ligands: PO4.8 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain C: K.30, Y.52, Y.56, F.137, Y.140 Ligands: PO4.15 Ligand excluded by PLIP CL.28: 6 residues within 4Å: Chain D: K.30, Y.52, Y.56, F.137, Y.140 Ligands: PO4.22 Ligand excluded by PLIP CL.35: 6 residues within 4Å: Chain E: K.30, Y.52, Y.56, F.137, Y.140 Ligands: PO4.29 Ligand excluded by PLIP CL.42: 6 residues within 4Å: Chain F: K.30, Y.52, Y.56, F.137, Y.140 Ligands: PO4.36 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hughes, R.C. et al., Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction. Acta Crystallogr.,Sect.F (2012)

Release Date

2012-01-04

Peptides

Tt-IPPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Tt-IPPase