SMTL ID : 4z73.1 (1 other biounit)

Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with a phosphate ion and an inorganic pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: K.136, D.137, E.139, K.142 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.137, A:E.139, A:K.142 MN.3: 4 residues within 4Å: Chain A: D.61, P.64, D.66, D.98 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.66, A:D.98 MN.4: 3 residues within 4Å: Chain A: Y.51, D.66 Ligands: PO4.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.66 MN.6: 4 residues within 4Å: Chain B: K.136, D.137, E.139, K.142 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.137, B:E.139, B:K.142 MN.7: 4 residues within 4Å: Chain B: E.17, Y.51, G.52, D.66 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.66 MN.8: 3 residues within 4Å: Chain B: D.61, D.66, D.98 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.66 MN.10: 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 MN.11: 6 residues within 4Å: Chain C: D.61, D.63, P.64, D.66, D.98 Ligands: MN.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.66 MN.12: 4 residues within 4Å: Chain C: Y.51, D.66 Ligands: PO4.9, MN.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:Y.51, C:D.66 MN.13: 4 residues within 4Å: Chain D: K.136, D.137, E.139, K.142 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.137, D:E.139, D:K.142 MN.14: 2 residues within 4Å: Chain D: D.61, D.66 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.66 MN.17: 4 residues within 4Å: Chain E: D.61, P.64, D.66, D.98 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.66, E:D.98 MN.19: 4 residues within 4Å: Chain F: E.17, Y.51, G.52, D.66 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.17, F:D.66

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

PO4.2: 6 residues within 4Å: Chain A: K.25, R.39, D.93, Y.135, K.136 Ligands: MN.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.135, A:Y.135 Salt bridges: A:K.25, A:R.39, A:K.136 PO4.9: 6 residues within 4Å: Chain C: K.25, R.39, D.93, Y.135, K.136 Ligands: MN.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.135 Salt bridges: C:K.25, C:R.39, C:K.136 PO4.15: 6 residues within 4Å: Chain D: K.25, R.39, Y.51, D.93, Y.135, K.136 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.51, D:Y.135 Salt bridges: D:K.25, D:R.39, D:K.136, D:K.142 PO4.16: 4 residues within 4Å: Chain E: K.25, R.39, E.94, Y.135 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:E.94, E:Y.135 Water bridges: E:E.27, E:D.38 Salt bridges: E:K.25, E:R.39, E:K.136, E:K.142 PO4.18: 6 residues within 4Å: Chain F: K.25, D.38, R.39, Y.135, K.136, K.142 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Y.135 Salt bridges: F:K.25, F:R.39, F:K.136, F:K.142

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

POP.5: 8 residues within 4Å: Chain B: K.25, E.27, R.39, Y.51, D.98, K.100, Y.135, K.136 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.27, B:D.98, B:Y.135 Water bridges: B:K.100, B:Y.135 Salt bridges: B:K.25, B:K.25, B:R.39, B:K.100, B:K.136

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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