SMTL ID : 4z74.1 (1 other biounit)

Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inorganic pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-hexamer

Ligands

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

POP.1: 8 residues within 4Å: Chain A: K.25, R.39, Y.51, D.98, K.100, Y.135, K.136 Ligands: CA.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.135, A:Y.135 Water bridges: A:K.25, A:D.66 Salt bridges: A:K.25, A:K.25, A:R.39, A:K.100, A:K.136 POP.6: 10 residues within 4Å: Chain B: K.25, E.27, R.39, Y.51, D.93, D.98, K.100, Y.135, K.136 Ligands: CA.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.51, B:Y.135, B:Y.135 Water bridges: B:K.25, B:R.39, B:K.136, B:K.136 Salt bridges: B:K.25, B:K.25, B:R.39, B:K.100, B:K.136 POP.11: 10 residues within 4Å: Chain C: K.25, R.39, Y.51, D.66, D.93, D.98, K.100, Y.135, K.136 Ligands: CA.15 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.51, C:D.98, C:Y.135 Water bridges: C:R.39 Salt bridges: C:K.25, C:K.25, C:R.39, C:K.100, C:K.136, C:K.136 POP.16: 10 residues within 4Å: Chain D: K.25, R.39, Y.51, D.93, D.98, K.100, Y.135, K.136, K.142 Ligands: CA.17 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Y.51, D:Y.135 Water bridges: D:K.25, D:Y.51, D:D.98, D:K.100 Salt bridges: D:K.25, D:K.25, D:R.39, D:K.100, D:K.136, D:K.142 POP.21: 9 residues within 4Å: Chain E: K.25, R.39, Y.51, D.93, D.98, K.100, Y.135, K.136 Ligands: CA.23 6 PLIP interactions: 6 interactions with chain E Salt bridges: E:K.25, E:K.25, E:R.39, E:K.100, E:K.136, E:K.136 POP.25: 8 residues within 4Å: Chain F: K.25, R.39, Y.51, D.93, D.98, Y.135, K.136 Ligands: CA.26 7 PLIP interactions: 7 interactions with chain F Water bridges: F:K.25 Salt bridges: F:K.25, F:K.25, F:R.39, F:K.100, F:K.136, F:K.142

22 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: K.136, D.137, E.139, K.142 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:K.136, A:D.137, A:E.139, A:K.142 CA.3: 3 residues within 4Å: Chain A: D.93, D.98 Ligands: POP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.98, H2O.1 CA.4: 4 residues within 4Å: Chain A: E.17, Y.51, G.52, D.66 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.17, A:D.66, H2O.3 CA.5: 2 residues within 4Å: Chain A: D.66, D.98 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.66, A:D.98, H2O.1, H2O.3 CA.7: 4 residues within 4Å: Chain B: E.17, Y.51, G.52, D.66 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.17, B:D.66, H2O.6 CA.8: 4 residues within 4Å: Chain B: D.93, D.98, K.136 Ligands: POP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.93, B:D.98, H2O.4 CA.9: 4 residues within 4Å: Chain B: K.136, D.137, E.139, K.142 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:K.136, B:D.137, B:E.139, B:K.142 CA.10: 2 residues within 4Å: Chain B: D.66, D.98 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.66, B:D.98, H2O.5 CA.12: 3 residues within 4Å: Chain C: P.64, D.66, D.98 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.66, H2O.8 CA.13: 4 residues within 4Å: Chain C: K.136, D.137, E.139, K.142 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.137, C:E.139, C:K.142 CA.14: 5 residues within 4Å: Chain C: E.17, Y.51, G.52, F.53, D.66 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.17, C:D.66, H2O.9 CA.15: 4 residues within 4Å: Chain C: D.93, D.98, K.136 Ligands: POP.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.93, C:D.98 CA.17: 5 residues within 4Å: Chain D: M.91, D.93, D.98, K.136 Ligands: POP.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.93, D:D.98 CA.18: 4 residues within 4Å: Chain D: K.136, D.137, E.139, K.142 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:K.136, D:D.137, D:E.139, D:K.142 CA.19: 4 residues within 4Å: Chain D: E.17, Y.51, G.52, D.66 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.17, D:G.52, D:D.66, H2O.13 CA.20: 4 residues within 4Å: Chain D: D.61, D.66, D.98, D.99 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.98, H2O.13, H2O.13 CA.22: 5 residues within 4Å: Chain E: E.17, Y.51, G.52, F.53, D.66 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.17, E:G.52, E:D.66 CA.23: 4 residues within 4Å: Chain E: D.93, D.98, K.136 Ligands: POP.21 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.93 CA.24: 4 residues within 4Å: Chain E: D.61, P.64, D.66, D.98 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.61, E:D.66, H2O.15 CA.26: 4 residues within 4Å: Chain F: D.93, D.98, K.136 Ligands: POP.25 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.93, F:D.98 CA.27: 2 residues within 4Å: Chain F: D.66, D.98 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.66, F:D.66, F:D.98, H2O.17, H2O.18 CA.28: 5 residues within 4Å: Chain F: E.17, Y.51, G.52, F.53, D.66 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.17, F:G.52, F:D.66, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pratt, A.C. et al., Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis. J.Struct.Biol. (2015)

Release Date

2015-08-26

Peptides

Inorganic pyrophosphatase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
E

Inorganic pyrophosphatase

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