SMTL ID : 5kde.1

Inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inhibitor 1 and inorganic pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-hexamer

Ligands

6 x 6RT: 2,4-bis(aziridin-1-yl)-6-(1-phenylpyrrol-2-yl)-1,3,5-triazine(Non-covalent)

6RT.1: 8 residues within 4Å: Chain A: P.72, R.110, W.111, V.114, D.119, P.121 Chain F: F.123 Ligands: 6RT.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.111, A:V.114, A:P.121 pi-Stacking: A:W.111 6RT.3: 8 residues within 4Å: Chain B: P.72, R.110, W.111, V.114, D.119, P.121 Chain E: F.123 Ligands: 6RT.9 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.111, B:V.114, B:P.121 pi-Stacking: B:W.111 6RT.5: 8 residues within 4Å: Chain C: P.72, R.110, W.111, V.114, D.119, P.121 Chain D: F.123 Ligands: 6RT.7 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.111, C:V.114, C:P.121 pi-Stacking: C:W.111 6RT.7: 8 residues within 4Å: Chain C: F.123 Chain D: P.72, R.110, W.111, V.114, D.119, P.121 Ligands: 6RT.5 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.111, D:V.114, D:P.121 pi-Stacking: D:W.111 6RT.9: 8 residues within 4Å: Chain B: F.123 Chain E: P.72, R.110, W.111, V.114, D.119, P.121 Ligands: 6RT.3 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:W.111, E:V.114, E:P.121 pi-Stacking: E:W.111 6RT.11: 8 residues within 4Å: Chain A: F.123 Chain F: P.72, R.110, W.111, V.114, D.119, P.121 Ligands: 6RT.1 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:W.111, F:V.114, F:P.121 pi-Stacking: F:W.111

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

POP.2: 8 residues within 4Å: Chain A: K.25, R.39, D.93, E.94, H.95, D.98, Y.135, K.136 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.51, A:D.93, A:D.93, A:E.94, A:Y.135 Water bridges: A:Y.51 Salt bridges: A:K.25, A:K.25, A:R.39, A:H.95, A:H.95, A:K.100, A:K.136, A:K.136, A:K.142 POP.4: 8 residues within 4Å: Chain B: K.25, R.39, D.93, E.94, H.95, D.98, Y.135, K.136 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Y.51, B:D.93, B:D.93, B:E.94, B:Y.135 Water bridges: B:Y.51 Salt bridges: B:K.25, B:K.25, B:R.39, B:H.95, B:H.95, B:K.100, B:K.136, B:K.136, B:K.142 POP.6: 8 residues within 4Å: Chain C: K.25, R.39, D.93, E.94, H.95, D.98, Y.135, K.136 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:Y.51, C:D.93, C:D.93, C:E.94, C:Y.135 Water bridges: C:Y.51 Salt bridges: C:K.25, C:K.25, C:R.39, C:H.95, C:H.95, C:K.100, C:K.136, C:K.136, C:K.142 POP.8: 8 residues within 4Å: Chain D: K.25, R.39, D.93, E.94, H.95, D.98, Y.135, K.136 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:D.93, D:E.94, D:Y.135 Water bridges: D:Y.51 Salt bridges: D:K.25, D:K.25, D:R.39, D:H.95, D:H.95, D:K.100, D:K.136, D:K.136, D:K.142 POP.10: 8 residues within 4Å: Chain E: K.25, R.39, D.93, E.94, H.95, D.98, Y.135, K.136 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:D.93, E:E.94, E:Y.135 Water bridges: E:Y.51 Salt bridges: E:K.25, E:K.25, E:R.39, E:H.95, E:H.95, E:K.100, E:K.136, E:K.136, E:K.142 POP.12: 8 residues within 4Å: Chain F: K.25, R.39, D.93, E.94, H.95, D.98, Y.135, K.136 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:D.93, F:E.94, F:Y.135 Water bridges: F:Y.51 Salt bridges: F:K.25, F:K.25, F:R.39, F:H.95, F:H.95, F:K.100, F:K.136, F:K.136, F:K.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, A.H. et al., Discovery of Allosteric and Selective Inhibitors of Inorganic Pyrophosphatase from Mycobacterium tuberculosis. ACS Chem. Biol. (2016)

Release Date

2016-09-28

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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