SMTL ID : 5ws8.1

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.221, E.223, D.247 Ligands: OXL.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.223, A:D.247, H2O.1, H2O.2 MG.3: 4 residues within 4Å: Chain B: K.221, E.223, D.247 Ligands: OXL.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.223, B:D.247, H2O.6, H2O.7 MG.5: 4 residues within 4Å: Chain C: K.221, E.223, D.247 Ligands: OXL.6 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.223, C:D.247, H2O.10, H2O.13 MG.7: 4 residues within 4Å: Chain D: K.221, E.223, D.247 Ligands: OXL.8 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.223, D:D.247, H2O.15, H2O.16

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 8 residues within 4Å: Chain A: K.221, E.223, A.244, R.245, G.246, D.247, T.279 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.246, A:D.247, A:T.279, A:T.279 Water bridges: A:R.36, A:R.36, A:R.36, A:K.221 Salt bridges: A:R.36, A:K.221, A:K.221 OXL.4: 8 residues within 4Å: Chain B: K.221, E.223, A.244, R.245, G.246, D.247, T.279 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.223, B:E.223, B:G.246, B:D.247, B:T.279 Water bridges: B:K.221 Salt bridges: B:R.36, B:K.221, B:K.221 OXL.6: 8 residues within 4Å: Chain C: K.221, E.223, A.244, R.245, G.246, D.247, T.279 Ligands: MG.5 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.246, C:D.247, C:T.279, C:T.279 Water bridges: C:R.36, C:R.36, C:K.221, C:K.221 Salt bridges: C:R.36, C:K.221, C:K.221 OXL.8: 9 residues within 4Å: Chain D: K.221, E.223, A.244, R.245, G.246, D.247, T.279, M.311 Ligands: MG.7 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.223, D:E.223, D:G.246, D:D.247, D:T.279 Water bridges: D:K.221, D:K.221 Salt bridges: D:R.36, D:K.221, D:K.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, W. et al., Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis. Nat Commun (2017)

Release Date

2017-11-15

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase

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