SMTL ID : 1wcf.1

1.54 A CRYSTAL STRUCTURE OF RV3628, MYCOBACTERIUM TUBERCULOSIS INORGANIC PYROPHOSPHATASE (PPASE) AT PH7.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-hexamer

Ligands

12 x K: POTASSIUM ION(Non-covalent)

K.1: 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.10 K.2: 3 residues within 4Å: Chain A: P.64, D.66, D.98 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.98, H2O.6, H2O.6, H2O.7 K.4: 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.20 K.5: 3 residues within 4Å: Chain B: P.64, D.66, D.98 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, H2O.17, H2O.17, H2O.18 K.7: 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.31 K.8: 3 residues within 4Å: Chain C: P.64, D.66, D.98 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.98, H2O.27, H2O.28, H2O.29 K.10: 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.42 K.11: 3 residues within 4Å: Chain D: P.64, D.66, D.98 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.98, H2O.38, H2O.38, H2O.40 K.13: 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.52 K.14: 3 residues within 4Å: Chain E: P.64, D.66, D.98 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.98, H2O.49, H2O.49, H2O.50 K.16: 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.63 K.17: 3 residues within 4Å: Chain F: P.64, D.66, D.98 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.98, H2O.60, H2O.60, H2O.61

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

PO4.3: 4 residues within 4Å: Chain A: K.25, R.39, Y.135, K.136 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.135 Water bridges: A:K.25, A:K.25, A:Y.51, A:Y.51, A:E.94, A:Y.135, A:K.136, A:K.136 Salt bridges: A:K.25, A:R.39, A:K.136 PO4.6: 4 residues within 4Å: Chain B: K.25, R.39, Y.135, K.136 11 PLIP interactions: 11 interactions with chain B Water bridges: B:K.25, B:K.25, B:Y.51, B:E.94, B:Y.135, B:Y.135, B:Y.135, B:K.136 Salt bridges: B:K.25, B:R.39, B:K.136 PO4.9: 4 residues within 4Å: Chain C: K.25, R.39, Y.135, K.136 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Y.135 Water bridges: C:K.25, C:K.25, C:Y.51, C:Y.51, C:E.94, C:Y.135, C:K.136, C:K.136 Salt bridges: C:K.25, C:R.39, C:K.136 PO4.12: 4 residues within 4Å: Chain D: K.25, R.39, Y.135, K.136 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Y.135 Water bridges: D:K.25, D:K.25, D:Y.51, D:Y.51, D:E.94, D:Y.135, D:K.136, D:K.136 Salt bridges: D:K.25, D:R.39, D:K.136 PO4.15: 4 residues within 4Å: Chain E: K.25, R.39, Y.135, K.136 11 PLIP interactions: 11 interactions with chain E Water bridges: E:K.25, E:K.25, E:Y.51, E:E.94, E:Y.135, E:Y.135, E:Y.135, E:K.136 Salt bridges: E:K.25, E:R.39, E:K.136 PO4.18: 4 residues within 4Å: Chain F: K.25, R.39, Y.135, K.136 11 PLIP interactions: 11 interactions with chain F Water bridges: F:K.25, F:K.25, F:Y.51, F:E.94, F:Y.135, F:Y.135, F:Y.135, F:K.136 Salt bridges: F:K.25, F:R.39, F:K.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benini, S. et al., Structure of the Mycobacterium Tuberculosis Soluble Inorganic Pyrophosphatase Rv3628 at Ph 7.0. Acta Crystallogr.,Sect.F (2011)

Release Date

2006-07-12

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