SMTL ID : 4z72.1

Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with two phosphate ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: K.25, Y.51, D.98, K.100, Y.135, K.136 Ligands: PO4.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.51, A:Y.135 Water bridges: A:K.25, A:K.25, A:K.25, A:R.39, A:Y.51, A:Y.51, A:D.66, A:D.66 Salt bridges: A:K.25, A:K.100, A:K.136 PO4.2: 7 residues within 4Å: Chain A: K.25, R.39, E.94, H.95, K.136, K.142 Ligands: PO4.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.94 Water bridges: A:D.38, A:R.39, A:R.39, A:R.39 Salt bridges: A:K.25, A:R.39, A:K.136, A:K.142 PO4.6: 7 residues within 4Å: Chain B: K.25, Y.51, D.98, K.100, Y.135, K.136 Ligands: PO4.7 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.51, B:Y.135 Water bridges: B:K.25, B:K.25, B:K.25, B:R.39, B:Y.51, B:Y.51, B:D.66, B:D.66 Salt bridges: B:K.25, B:K.100, B:K.136 PO4.7: 7 residues within 4Å: Chain B: K.25, R.39, E.94, H.95, K.136, K.142 Ligands: PO4.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.94 Water bridges: B:D.38, B:R.39, B:R.39, B:R.39 Salt bridges: B:K.25, B:R.39, B:K.136, B:K.142 PO4.11: 7 residues within 4Å: Chain C: K.25, Y.51, D.98, K.100, Y.135, K.136 Ligands: PO4.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.51, C:Y.135 Water bridges: C:K.25, C:K.25, C:K.25, C:R.39, C:Y.51, C:Y.51, C:D.66, C:D.66 Salt bridges: C:K.25, C:K.100, C:K.136 PO4.12: 7 residues within 4Å: Chain C: K.25, R.39, E.94, H.95, K.136, K.142 Ligands: PO4.11 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.94 Water bridges: C:D.38, C:R.39, C:R.39, C:R.39 Salt bridges: C:K.25, C:R.39, C:K.136, C:K.142 PO4.16: 7 residues within 4Å: Chain D: K.25, Y.51, D.98, K.100, Y.135, K.136 Ligands: PO4.17 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.51, D:Y.51 Water bridges: D:K.25, D:K.25, D:K.25, D:E.27, D:E.27, D:Y.51, D:D.66, D:D.66 Salt bridges: D:K.25, D:K.100, D:K.136 PO4.17: 7 residues within 4Å: Chain D: K.25, R.39, E.94, H.95, K.136, K.142 Ligands: PO4.16 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:E.94 Water bridges: D:D.38, D:R.39, D:R.39, D:R.39 Salt bridges: D:K.25, D:R.39, D:K.136, D:K.142 PO4.21: 7 residues within 4Å: Chain E: K.25, Y.51, D.98, K.100, Y.135, K.136 Ligands: PO4.22 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:Y.51, E:Y.51 Water bridges: E:K.25, E:K.25, E:K.25, E:E.27, E:E.27, E:Y.51, E:D.66, E:D.66 Salt bridges: E:K.25, E:K.100, E:K.136 PO4.22: 7 residues within 4Å: Chain E: K.25, R.39, E.94, H.95, K.136, K.142 Ligands: PO4.21 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:E.94 Water bridges: E:D.38, E:R.39, E:R.39, E:R.39 Salt bridges: E:K.25, E:R.39, E:K.136, E:K.142 PO4.26: 7 residues within 4Å: Chain F: K.25, Y.51, D.98, K.100, Y.135, K.136 Ligands: PO4.27 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Y.51, F:Y.51 Water bridges: F:K.25, F:K.25, F:K.25, F:E.27, F:E.27, F:Y.51, F:D.66, F:D.66 Salt bridges: F:K.25, F:K.100, F:K.136 PO4.27: 7 residues within 4Å: Chain F: K.25, R.39, E.94, H.95, K.136, K.142 Ligands: PO4.26 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:E.94 Water bridges: F:D.38, F:R.39, F:R.39, F:R.39 Salt bridges: F:K.25, F:R.39, F:K.136, F:K.142

18 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: E.17, D.66 No protein-ligand interaction detected (PLIP) CA.4: 2 residues within 4Å: Chain A: E.27, D.38 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.27, H2O.1, H2O.1 CA.5: 4 residues within 4Å: Chain A: K.136, D.137, E.139, K.142 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.136, A:E.139, A:K.142, H2O.1 CA.8: 2 residues within 4Å: Chain B: E.17, D.66 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain B: E.27, D.38 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.27, H2O.2, H2O.3 CA.10: 4 residues within 4Å: Chain B: K.136, D.137, E.139, K.142 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.136, B:E.139, B:K.142, H2O.3 CA.13: 2 residues within 4Å: Chain C: E.17, D.66 No protein-ligand interaction detected (PLIP) CA.14: 2 residues within 4Å: Chain C: E.27, D.38 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.27, H2O.4, H2O.4 CA.15: 4 residues within 4Å: Chain C: K.136, D.137, E.139, K.142 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:K.136, C:E.139, C:K.142, H2O.4 CA.18: 2 residues within 4Å: Chain D: E.17, D.66 No protein-ligand interaction detected (PLIP) CA.19: 2 residues within 4Å: Chain D: E.27, D.38 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.27, H2O.5, H2O.5 CA.20: 4 residues within 4Å: Chain D: K.136, D.137, E.139, K.142 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:K.136, D:E.139, D:K.142, H2O.5 CA.23: 2 residues within 4Å: Chain E: E.17, D.66 No protein-ligand interaction detected (PLIP) CA.24: 2 residues within 4Å: Chain E: E.27, D.38 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.27, H2O.6, H2O.6 CA.25: 4 residues within 4Å: Chain E: K.136, D.137, E.139, K.142 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:K.136, E:E.139, E:K.142, H2O.6 CA.28: 2 residues within 4Å: Chain F: E.17, D.66 No protein-ligand interaction detected (PLIP) CA.29: 2 residues within 4Å: Chain F: E.27, D.38 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.27, H2O.7, H2O.7 CA.30: 4 residues within 4Å: Chain F: K.136, D.137, E.139, K.142 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:K.136, F:E.139, F:K.142, H2O.7

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
A

C
A

D
A

E
A

F
A

Inorganic pyrophosphatase

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