SMTL ID : 5wsa.1

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate and allosteric activator Glucose 6-Phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

Ligands

4 x G6P: 6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G6P.1: 10 residues within 4Å: Chain A: L.236, E.270, N.271, H.348, P.350, R.351, T.352, G.355, R.385, R.388 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.351, A:T.352, A:T.352, A:T.352, A:T.352, A:G.355 Salt bridges: A:H.348, A:R.385, A:R.385, A:R.388 G6P.5: 10 residues within 4Å: Chain B: L.236, E.270, N.271, H.348, P.350, R.351, T.352, G.355, R.385, R.388 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.270, B:R.351, B:T.352, B:G.355 Salt bridges: B:H.348, B:R.385, B:R.385, B:R.388 G6P.9: 11 residues within 4Å: Chain C: L.236, E.270, N.271, K.273, H.348, P.350, R.351, T.352, G.355, R.385, R.388 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.351, C:T.352, C:T.352, C:T.352 Salt bridges: C:H.348, C:R.385, C:R.385, C:R.388 G6P.13: 10 residues within 4Å: Chain D: L.236, E.270, N.271, H.348, P.350, R.351, T.352, G.355, R.385, R.388 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.351, D:T.352 Salt bridges: D:H.348, D:R.385, D:R.385, D:R.388

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.221, E.223, D.247 Ligands: OXL.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.223, A:D.247, H2O.1 MG.6: 4 residues within 4Å: Chain B: K.221, E.223, D.247 Ligands: OXL.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.223, B:D.247, H2O.2 MG.10: 3 residues within 4Å: Chain C: E.223, D.247 Ligands: OXL.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.223, C:D.247, H2O.4, H2O.4 MG.14: 4 residues within 4Å: Chain D: F.195, E.223, D.247 Ligands: OXL.15 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.223, D:D.247, H2O.6

4 x OXL: OXALATE ION(Non-covalent)

OXL.3: 8 residues within 4Å: Chain A: K.221, E.223, A.244, R.245, G.246, D.247, T.279 Ligands: MG.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.246, A:D.247, A:T.279, A:T.279 Salt bridges: A:R.36, A:K.221, A:K.221 OXL.7: 8 residues within 4Å: Chain B: K.221, E.223, A.244, R.245, G.246, D.247, T.279 Ligands: MG.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.246, B:D.247 Water bridges: B:K.221 Salt bridges: B:K.221, B:K.221 OXL.11: 7 residues within 4Å: Chain C: R.36, K.221, E.223, A.244, D.247, T.279 Ligands: MG.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.247, C:T.279 Water bridges: C:K.221, C:K.221 Salt bridges: C:R.36, C:K.221, C:K.221 OXL.15: 7 residues within 4Å: Chain D: R.36, K.221, E.223, A.244, D.247, T.279 Ligands: MG.14 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.223 Water bridges: D:R.36, D:R.36, D:K.221 Salt bridges: D:R.36, D:K.221, D:K.221

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

PO4.4: 9 residues within 4Å: Chain A: R.354, T.377, Q.378, S.379, G.380, D.381, T.382, V.459, G.460 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.378, A:S.379, A:G.380, A:D.381, A:T.382, A:T.382, A:T.382, A:G.460 Salt bridges: A:R.354 PO4.8: 11 residues within 4Å: Chain B: R.354, F.376, T.377, Q.378, S.379, G.380, D.381, T.382, T.458, V.459, G.460 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.377, B:T.377, B:T.377, B:Q.378, B:S.379, B:G.380, B:D.381, B:T.382, B:T.382, B:G.460 Salt bridges: B:R.354 PO4.12: 9 residues within 4Å: Chain C: R.354, T.377, Q.378, S.379, G.380, T.382, V.459, G.460, T.462 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.377, C:Q.378, C:S.379, C:S.379, C:S.379, C:G.380, C:D.381, C:T.382, C:T.382, C:G.460, C:T.462 Salt bridges: C:R.354 PO4.16: 10 residues within 4Å: Chain D: R.354, F.376, T.377, Q.378, S.379, G.380, D.381, T.382, G.460, T.462 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:F.376, D:T.377, D:Q.378, D:S.379, D:G.380, D:D.381, D:T.382, D:G.460, D:T.462, D:T.462 Salt bridges: D:R.354

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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