SMTL ID : 1sxv.1

1.3A Crystal structure of rv3628, Mycobacterium tuberculosis inorganic pyrophosphatase (PPase) at pH5.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-hexamer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: K.26, R.40, H.96, Y.136, K.137 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.136 Water bridges: A:K.26, A:K.26, A:Y.52, A:Y.52, A:E.95, A:H.96, A:H.96, A:Y.136 Salt bridges: A:K.26, A:R.40, A:H.96, A:K.137 SO4.5: 5 residues within 4Å: Chain B: K.26, R.40, H.96, Y.136, K.137 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.136 Water bridges: B:K.26, B:K.26, B:Y.52, B:Y.52, B:E.95, B:H.96, B:H.96, B:Y.136 Salt bridges: B:K.26, B:R.40, B:H.96, B:K.137 SO4.9: 5 residues within 4Å: Chain C: K.26, R.40, H.96, Y.136, K.137 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.136 Water bridges: C:K.26, C:K.26, C:Y.52, C:Y.52, C:E.95, C:H.96, C:H.96, C:Y.136 Salt bridges: C:K.26, C:R.40, C:H.96, C:K.137 SO4.13: 5 residues within 4Å: Chain D: K.26, R.40, H.96, Y.136, K.137 11 PLIP interactions: 11 interactions with chain D Water bridges: D:K.26, D:K.26, D:Y.52, D:E.95, D:H.96, D:H.96, D:Y.136 Salt bridges: D:K.26, D:R.40, D:H.96, D:K.137 SO4.17: 5 residues within 4Å: Chain E: K.26, R.40, H.96, Y.136, K.137 11 PLIP interactions: 11 interactions with chain E Water bridges: E:K.26, E:K.26, E:Y.52, E:E.95, E:H.96, E:H.96, E:Y.136 Salt bridges: E:K.26, E:R.40, E:H.96, E:K.137 SO4.21: 5 residues within 4Å: Chain F: K.26, R.40, H.96, Y.136, K.137 11 PLIP interactions: 11 interactions with chain F Water bridges: F:K.26, F:K.26, F:Y.52, F:E.95, F:H.96, F:H.96, F:Y.136 Salt bridges: F:K.26, F:R.40, F:H.96, F:K.137

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: P.122, A.123, F.124 Ligand excluded by PLIP GOL.3: 3 residues within 4Å: Chain A: R.111, W.112, H.114 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: P.20, Q.74, V.76, F.77 Chain B: Q.23 Chain C: F.77 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain B: P.122, A.123, F.124 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain B: R.111, W.112, H.114 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: F.77 Chain B: P.20, Q.74, V.76, F.77 Chain C: Q.23 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain C: P.122, A.123, F.124 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain C: R.111, W.112, H.114 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: Q.23 Chain B: F.77 Chain C: P.20, Q.74, V.76, F.77 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain D: P.122, A.123, F.124 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain D: R.111, W.112, H.114 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain D: P.20, Q.74, V.76, F.77 Chain E: Q.23 Chain F: F.77 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain E: P.122, A.123, F.124 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain E: R.111, W.112, H.114 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain D: F.77 Chain E: P.20, Q.74, V.76, F.77 Chain F: Q.23 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain F: P.122, A.123, F.124 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain F: R.111, W.112, H.114 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain D: Q.23 Chain E: F.77 Chain F: P.20, Q.74, V.76, F.77 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benini, S. et al., Mycobacterium tuberculosis Rv3628, yet another inorganic pyrophosphatase or a possible drug target?. To be Published

Release Date

2005-04-12

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