SMTL ID : 5kdf.1

Inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inhibitor 6 and inorganic pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-hexamer

Ligands

6 x 6RU: ~{N}2,~{N}2,~{N}4,~{N}4-tetramethyl-6-(1-phenylpyrrol-2-yl)-1,3,5-triazine-2,4-diamine(Non-covalent)

6RU.1: 9 residues within 4Å: Chain A: P.72, R.110, W.111 Chain F: V.114, D.119, P.121, F.123, E.124 Ligands: 6RU.26 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:P.72, F:F.123 pi-Stacking: A:W.111, A:W.111 6RU.6: 9 residues within 4Å: Chain B: P.72, R.110, W.111 Chain E: V.114, D.119, P.121, F.123, E.124 Ligands: 6RU.21 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:P.72, E:F.123 pi-Stacking: B:W.111, B:W.111 6RU.11: 9 residues within 4Å: Chain C: P.72, R.110, W.111 Chain D: V.114, D.119, P.121, F.123, E.124 Ligands: 6RU.16 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.123, C:P.72 pi-Stacking: C:W.111, C:W.111 6RU.16: 9 residues within 4Å: Chain C: V.114, D.119, P.121, F.123, E.124 Chain D: P.72, R.110, W.111 Ligands: 6RU.11 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.72, C:F.123 pi-Stacking: D:W.111, D:W.111 6RU.21: 9 residues within 4Å: Chain B: V.114, D.119, P.121, F.123, E.124 Chain E: P.72, R.110, W.111 Ligands: 6RU.6 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:F.123, E:P.72 pi-Stacking: E:W.111, E:W.111 6RU.26: 9 residues within 4Å: Chain A: V.114, D.119, P.121, F.123, E.124 Chain F: P.72, R.110, W.111 Ligands: 6RU.1 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:P.72, A:F.123 pi-Stacking: F:W.111, F:W.111

18 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.27, D.38 Ligands: POP.5 No protein-ligand interaction detected (PLIP) CA.3: 4 residues within 4Å: Chain A: K.136, D.137, E.139, K.142 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.139, A:K.142 CA.4: 1 residues within 4Å: Chain A: E.17 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain B: E.27, D.38 Ligands: POP.10 No protein-ligand interaction detected (PLIP) CA.8: 4 residues within 4Å: Chain B: K.136, D.137, E.139, K.142 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.139, B:K.142 CA.9: 1 residues within 4Å: Chain B: E.17 No protein-ligand interaction detected (PLIP) CA.12: 3 residues within 4Å: Chain C: E.27, D.38 Ligands: POP.15 No protein-ligand interaction detected (PLIP) CA.13: 4 residues within 4Å: Chain C: K.136, D.137, E.139, K.142 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.139, C:K.142 CA.14: 1 residues within 4Å: Chain C: E.17 No protein-ligand interaction detected (PLIP) CA.17: 3 residues within 4Å: Chain D: E.27, D.38 Ligands: POP.20 No protein-ligand interaction detected (PLIP) CA.18: 4 residues within 4Å: Chain D: K.136, D.137, E.139, K.142 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.139, D:K.142 CA.19: 1 residues within 4Å: Chain D: E.17 No protein-ligand interaction detected (PLIP) CA.22: 3 residues within 4Å: Chain E: E.27, D.38 Ligands: POP.25 No protein-ligand interaction detected (PLIP) CA.23: 4 residues within 4Å: Chain E: K.136, D.137, E.139, K.142 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.139, E:K.142 CA.24: 1 residues within 4Å: Chain E: E.17 No protein-ligand interaction detected (PLIP) CA.27: 3 residues within 4Å: Chain F: E.27, D.38 Ligands: POP.30 No protein-ligand interaction detected (PLIP) CA.28: 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 CA.29: 1 residues within 4Å: Chain F: E.17 No protein-ligand interaction detected (PLIP)

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

POP.5: 10 residues within 4Å: Chain A: K.25, R.39, Y.51, D.93, E.94, D.98, Y.135, K.136, K.142 Ligands: CA.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.51, A:D.93, A:D.93, A:E.94, A:Y.135 Water bridges: A:D.66, A:D.98 Salt bridges: A:K.25, A:K.25, A:R.39, A:K.100, A:K.136, A:K.136, A:K.142 POP.10: 10 residues within 4Å: Chain B: K.25, R.39, Y.51, D.93, E.94, D.98, Y.135, K.136, K.142 Ligands: CA.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Y.51, B:D.93, B:D.93, B:E.94, B:Y.135 Water bridges: B:D.66, B:D.98 Salt bridges: B:K.25, B:K.25, B:R.39, B:K.100, B:K.136, B:K.136, B:K.142 POP.15: 10 residues within 4Å: Chain C: K.25, R.39, Y.51, D.93, E.94, D.98, Y.135, K.136, K.142 Ligands: CA.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Y.51, C:D.93, C:D.93, C:E.94, C:Y.135 Water bridges: C:D.66, C:D.98 Salt bridges: C:K.25, C:K.25, C:R.39, C:K.100, C:K.136, C:K.136, C:K.142 POP.20: 10 residues within 4Å: Chain D: K.25, R.39, Y.51, D.93, E.94, D.98, Y.135, K.136, K.142 Ligands: CA.17 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:D.93, D:E.94 Water bridges: D:D.66, D:D.98 Salt bridges: D:K.25, D:K.25, D:R.39, D:K.100, D:K.136, D:K.136, D:K.142 POP.25: 10 residues within 4Å: Chain E: K.25, R.39, Y.51, D.93, E.94, D.98, Y.135, K.136, K.142 Ligands: CA.22 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:D.93, E:E.94 Water bridges: E:D.66, E:D.98 Salt bridges: E:K.25, E:K.25, E:R.39, E:K.100, E:K.136, E:K.136, E:K.142 POP.30: 10 residues within 4Å: Chain F: K.25, R.39, Y.51, D.93, E.94, D.98, Y.135, K.136, K.142 Ligands: CA.27 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:D.93, F:E.94 Water bridges: F:D.66, F:D.98 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

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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