SMTL ID : 3q4w.1

The structure of archaeal inorganic pyrophosphatase in complex with substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-hexamer

Ligands

18 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.98, D.103 Ligands: CA.2, POP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.103, H2O.2, H2O.5 CA.2: 6 residues within 4Å: Chain A: D.66, D.71, D.103 Ligands: CA.1, POP.3, NA.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.66, A:D.71, A:D.103, A:D.103, H2O.2 CA.6: 3 residues within 4Å: Chain A: D.66, D.68 Ligands: POP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.68, H2O.4, H2O.10, H2O.10, H2O.11 CA.7: 4 residues within 4Å: Chain B: D.98, D.103 Ligands: CA.8, POP.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.103, H2O.12, H2O.15 CA.8: 6 residues within 4Å: Chain B: D.66, D.71, D.103 Ligands: CA.7, POP.9, NA.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.66, B:D.71, B:D.103, B:D.103, H2O.12 CA.12: 3 residues within 4Å: Chain B: D.66, D.68 Ligands: POP.9 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.68, H2O.14, H2O.20, H2O.21, H2O.21 CA.13: 4 residues within 4Å: Chain C: D.98, D.103 Ligands: CA.14, POP.15 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.98, C:D.103, H2O.22, H2O.25 CA.14: 6 residues within 4Å: Chain C: D.66, D.71, D.103 Ligands: CA.13, POP.15, NA.17 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.66, C:D.71, C:D.103, C:D.103, H2O.22 CA.18: 3 residues within 4Å: Chain C: D.66, D.68 Ligands: POP.15 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.68, H2O.24, H2O.31, H2O.31, H2O.31 CA.19: 4 residues within 4Å: Chain D: D.98, D.103 Ligands: CA.20, POP.21 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.98, D:D.103, H2O.32, H2O.35 CA.20: 6 residues within 4Å: Chain D: D.66, D.71, D.103 Ligands: CA.19, POP.21, NA.23 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.66, D:D.71, D:D.103, D:D.103, H2O.33 CA.24: 3 residues within 4Å: Chain D: D.66, D.68 Ligands: POP.21 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.68, H2O.34, H2O.41, H2O.41, H2O.41 CA.25: 4 residues within 4Å: Chain E: D.98, D.103 Ligands: CA.26, POP.27 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.98, E:D.103, H2O.42, H2O.45 CA.26: 6 residues within 4Å: Chain E: D.66, D.71, D.103 Ligands: CA.25, POP.27, NA.29 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.66, E:D.71, E:D.103, E:D.103, H2O.43 CA.30: 3 residues within 4Å: Chain E: D.66, D.68 Ligands: POP.27 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.68, H2O.44, H2O.51, H2O.51, H2O.51 CA.31: 4 residues within 4Å: Chain F: D.98, D.103 Ligands: CA.32, POP.33 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.98, F:D.103, H2O.52, H2O.55 CA.32: 6 residues within 4Å: Chain F: D.66, D.71, D.103 Ligands: CA.31, POP.33, NA.35 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.66, F:D.71, F:D.103, F:D.103, H2O.53 CA.36: 3 residues within 4Å: Chain F: D.66, D.68 Ligands: POP.33 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.68, H2O.55, H2O.61, H2O.61, H2O.61

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

POP.3: 14 residues within 4Å: Chain A: K.30, R.44, Y.56, D.66, D.71, D.98, D.103, Y.140, K.141 Ligands: CA.1, CA.2, BR.4, NA.5, CA.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.71, A:D.71 Water bridges: A:K.30, A:K.105, A:K.105, A:K.141 Salt bridges: A:K.30, A:K.30, A:R.44, A:K.105, A:K.141 POP.9: 14 residues within 4Å: Chain B: K.30, R.44, Y.56, D.66, D.71, D.98, D.103, Y.140, K.141 Ligands: CA.7, CA.8, BR.10, NA.11, CA.12 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.71, B:D.71 Water bridges: B:K.30, B:K.105, B:K.105, B:K.141 Salt bridges: B:K.30, B:K.30, B:R.44, B:K.105, B:K.141 POP.15: 14 residues within 4Å: Chain C: K.30, R.44, Y.56, D.66, D.71, D.98, D.103, Y.140, K.141 Ligands: CA.13, CA.14, BR.16, NA.17, CA.18 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:D.71, C:D.71 Water bridges: C:K.30, C:K.105, C:K.105, C:K.141 Salt bridges: C:K.30, C:K.30, C:R.44, C:K.105, C:K.141 POP.21: 14 residues within 4Å: Chain D: K.30, R.44, Y.56, D.66, D.71, D.98, D.103, Y.140, K.141 Ligands: CA.19, CA.20, BR.22, NA.23, CA.24 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Y.56, D:D.66, D:D.71, D:D.71, D:Y.140 Water bridges: D:K.30, D:Y.52, D:D.68, D:K.105, D:K.105, D:K.141 Salt bridges: D:K.30, D:K.30, D:R.44, D:K.105, D:K.141 POP.27: 14 residues within 4Å: Chain E: K.30, R.44, Y.56, D.66, D.71, D.98, D.103, Y.140, K.141 Ligands: CA.25, CA.26, BR.28, NA.29, CA.30 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:Y.56, E:D.66, E:D.71, E:D.71, E:Y.140 Water bridges: E:K.30, E:Y.52, E:D.68, E:K.105, E:K.105, E:K.141 Salt bridges: E:K.30, E:K.30, E:R.44, E:K.105, E:K.141 POP.33: 14 residues within 4Å: Chain F: K.30, R.44, Y.56, D.66, D.71, D.98, D.103, Y.140, K.141 Ligands: CA.31, CA.32, BR.34, NA.35, CA.36 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:Y.56, F:D.66, F:D.71, F:D.71, F:Y.140 Water bridges: F:K.30, F:Y.52, F:D.68, F:K.105, F:K.105, F:K.141 Salt bridges: F:K.30, F:K.30, F:R.44, F:K.105, F:K.141

6 x BR: BROMIDE ION(Non-covalent)

BR.4: 7 residues within 4Å: Chain A: E.22, Y.56, G.57, I.58, D.71 Ligands: POP.3, NA.5 Ligand excluded by PLIP BR.10: 7 residues within 4Å: Chain B: E.22, Y.56, G.57, I.58, D.71 Ligands: POP.9, NA.11 Ligand excluded by PLIP BR.16: 7 residues within 4Å: Chain C: E.22, Y.56, G.57, I.58, D.71 Ligands: POP.15, NA.17 Ligand excluded by PLIP BR.22: 7 residues within 4Å: Chain D: E.22, Y.56, G.57, I.58, D.71 Ligands: POP.21, NA.23 Ligand excluded by PLIP BR.28: 7 residues within 4Å: Chain E: E.22, Y.56, G.57, I.58, D.71 Ligands: POP.27, NA.29 Ligand excluded by PLIP BR.34: 7 residues within 4Å: Chain F: E.22, Y.56, G.57, I.58, D.71 Ligands: POP.33, NA.35 Ligand excluded by PLIP

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

NA.5: 4 residues within 4Å: Chain A: D.71 Ligands: CA.2, POP.3, BR.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.22, A:E.22, A:E.22 NA.11: 4 residues within 4Å: Chain B: D.71 Ligands: CA.8, POP.9, BR.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.22 NA.17: 4 residues within 4Å: Chain C: D.71 Ligands: CA.14, POP.15, BR.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.71 NA.23: 4 residues within 4Å: Chain D: D.71 Ligands: CA.20, POP.21, BR.22 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.22 NA.29: 4 residues within 4Å: Chain E: D.71 Ligands: CA.26, POP.27, BR.28 2 PLIP interactions: 2 interactions with chain E Water bridges: E:E.22, E:E.22 NA.35: 4 residues within 4Å: Chain F: D.71 Ligands: CA.32, POP.33, BR.34 2 PLIP interactions: 2 interactions with chain F Water bridges: F:E.22, F:E.22

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

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