SMTL ID : 4z73.2 (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

14 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.2: 4 residues within 4Å: Chain A: D.61, P.64, D.66, D.98 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.66, A:D.98, A:D.98 MN.4: 3 residues within 4Å: Chain A: Y.51, D.66, D.98 No protein-ligand interaction detected (PLIP) MN.5: 4 residues within 4Å: Chain B: D.61, P.64, D.66, D.98 1 PLIP interactions: 1 interactions with chain B Metal complexes: B: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.9: 3 residues within 4Å: Chain C: D.61, P.64, D.66 1 PLIP interactions: 1 interactions with chain C Metal complexes: C: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: 4 residues within 4Å: Chain C: Y.51, D.66, K.100 Ligands: PO4.8 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Y.51, H2O.1 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.15: 3 residues within 4Å: Chain E: E.17, Y.51, D.66 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.66 MN.16: 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.66 MN.18: 4 residues within 4Å: Chain F: K.136, D.137, E.139, K.142 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.139, F:K.142 MN.19: 4 residues within 4Å: Chain F: E.17, Y.51, D.66 Ligands: POP.17 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:Y.51, F:D.66 MN.20: 3 residues within 4Å: Chain F: D.66, D.98 Ligands: POP.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.66

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

PO4.3: 5 residues within 4Å: Chain A: K.25, R.39, Y.135, K.136, K.142 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:K.25, A:R.39, A:K.136, A:K.142 PO4.7: 4 residues within 4Å: Chain B: K.25, R.39, Y.135, K.136 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.135 Salt bridges: B:K.25, B:R.39, B:K.136 PO4.8: 7 residues within 4Å: Chain C: K.25, R.39, D.93, D.98, Y.135, K.136 Ligands: MN.11 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.27, C:E.27, C:D.98, C:D.98, C:Y.135 Salt bridges: C:K.25, C:R.39, C:K.100, C:K.136 PO4.12: 4 residues within 4Å: Chain D: K.25, R.39, Y.135, K.136 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.135, D:Y.135 Water bridges: D:E.27, D:R.39 Salt bridges: D:K.25, D:R.39, D:K.136

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

POP.14: 5 residues within 4Å: Chain E: K.25, R.39, Y.51, K.100, Y.135 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:Y.51, E:Y.51 Salt bridges: E:K.25, E:K.25, E:R.39, E:K.100, E:K.136 POP.17: 8 residues within 4Å: Chain F: K.25, R.39, Y.51, D.98, Y.135, K.136 Ligands: MN.19, MN.20 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:Y.135 Water bridges: F:E.27, F:D.38 Salt bridges: F:K.25, F:K.25, F:R.39, F:K.100, F:K.136, F:K.136, F:K.142

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
G

B
H

C
I

D
J

E
K

F
L

Inorganic pyrophosphatase

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