SMTL ID : 5wsc.1

Crystal of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, soaked with allosteric activators AMP and Glucose 6-Phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 25 residues within 4Å: Chain A: R.354, F.376, T.377, Q.378, S.379, D.381, T.382, F.398, A.400, W.401, V.419, P.420, K.421, M.422, M.428, A.452, G.453, P.455, P.456, G.457, T.458, V.459, G.460, S.461, T.462 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Q.378, A:S.379, A:S.379, A:D.381, A:T.382, A:T.382, A:P.420, A:M.422, A:G.453, A:G.457, A:G.460, A:S.461, A:T.462 Salt bridges: A:R.354 pi-Stacking: A:W.401, A:W.401 AMP.5: 25 residues within 4Å: Chain B: R.354, F.376, T.377, Q.378, S.379, G.380, D.381, T.382, T.399, A.400, W.401, V.419, P.420, K.421, M.422, M.428, G.453, P.455, P.456, G.457, T.458, V.459, G.460, S.461, T.462 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:T.377, B:Q.378, B:S.379, B:G.380, B:D.381, B:T.382, B:A.400, B:P.420, B:M.422, B:G.453, B:G.457, B:G.460, B:S.461, B:S.461, B:T.462, B:T.462 Water bridges: B:T.382 Salt bridges: B:R.354 pi-Stacking: B:F.376, B:W.401 AMP.10: 24 residues within 4Å: Chain C: R.354, F.376, T.377, Q.378, S.379, G.380, D.381, T.382, T.399, A.400, W.401, V.419, P.420, M.422, M.428, G.453, P.455, P.456, G.457, T.458, V.459, G.460, S.461, T.462 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:Q.378, C:S.379, C:S.379, C:G.380, C:D.381, C:T.382, C:T.382, C:A.400, C:P.420, C:M.422, C:G.453, C:G.457, C:T.458, C:G.460, C:S.461, C:S.461, C:T.462 Salt bridges: C:R.354 pi-Stacking: C:W.401 AMP.15: 26 residues within 4Å: Chain D: R.354, F.376, T.377, Q.378, S.379, G.380, D.381, T.382, F.398, T.399, A.400, W.401, V.419, P.420, K.421, M.422, M.428, G.453, P.455, P.456, G.457, T.458, V.459, G.460, S.461, T.462 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:T.377, D:Q.378, D:S.379, D:S.379, D:G.380, D:D.381, D:T.382, D:A.400, D:P.420, D:M.422, D:G.453, D:G.457, D:T.458, D:G.460, D:T.462 Salt bridges: D:R.354 pi-Stacking: D:W.401, D:W.401

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

G6P.2: 11 residues within 4Å: Chain A: L.236, E.270, N.271, K.273, H.348, P.350, R.351, T.352, G.355, R.385, R.388 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.351, A:T.352, A:T.352 Salt bridges: A:H.348, A:R.385, A:R.385, A:R.388 G6P.6: 11 residues within 4Å: Chain B: L.236, E.270, N.271, K.273, H.348, P.350, R.351, T.352, G.355, R.385, R.388 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.270, B:R.351, B:T.352 Salt bridges: B:H.348, B:R.385, B:R.385, B:R.388 G6P.11: 10 residues within 4Å: Chain C: L.236, E.270, N.271, K.273, H.348, P.350, R.351, T.352, R.385, R.388 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.351, C:T.352, C:T.352 Salt bridges: C:K.273, C:H.348, C:R.385, C:R.385, C:R.388 G6P.16: 11 residues within 4Å: Chain D: 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 D Hydrogen bonds: D:E.270, D:R.351, D:T.352, D:G.355 Salt bridges: D:H.348, D:R.385, D:R.385, D:R.388

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.221, E.223, D.247 Ligands: OXL.4 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.7: 4 residues within 4Å: Chain B: K.221, E.223, D.247 Ligands: OXL.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.223, B:D.247, H2O.5, H2O.6 MG.12: 3 residues within 4Å: Chain C: E.223, D.247 Ligands: OXL.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.223, C:D.247, H2O.8, H2O.8 MG.17: 3 residues within 4Å: Chain D: E.223, D.247 Ligands: OXL.18 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.223, D:D.247, H2O.11, H2O.12

4 x OXL: OXALATE ION(Non-covalent)

OXL.4: 8 residues within 4Å: Chain A: K.221, E.223, A.244, R.245, G.246, D.247, T.279 Ligands: MG.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.246, A:D.247, A:D.247, A:D.247, A:T.279 Salt bridges: A:R.36, A:K.221, A:K.221 OXL.8: 8 residues within 4Å: Chain B: K.221, E.223, A.244, R.245, G.246, D.247, T.279 Ligands: MG.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.223, B:E.223, B:G.246, B:D.247 Water bridges: B:K.221, B:K.221 Salt bridges: B:R.36, B:K.221 OXL.13: 9 residues within 4Å: Chain C: K.221, E.223, A.244, R.245, G.246, D.247, T.279, M.311 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.246, C:D.247, C:T.279, C:T.279, C:T.279 Water bridges: C:K.221 Salt bridges: C:R.36, C:K.221 OXL.18: 9 residues within 4Å: Chain D: K.221, E.223, A.244, R.245, G.246, D.247, T.279, M.311 Ligands: MG.17 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.223, D:G.246, D:D.247, D:T.279 Salt bridges: D:R.36, D:K.221, D:K.221

1 x K: POTASSIUM ION(Non-covalent)

K.9: 7 residues within 4Å: Chain B: N.38, S.40, D.70, L.71, Q.72, S.194, K.221 No protein-ligand interaction detected (PLIP)

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

PO4.14: 5 residues within 4Å: Chain C: N.38, S.40, H.41, K.75, R.77 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.38 Salt bridges: C:H.41, C:K.75, C:R.77 PO4.19: 5 residues within 4Å: Chain D: N.38, H.41, K.75, R.77, K.158 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.38 Water bridges: D:H.41, D:K.158 Salt bridges: D:H.41, D:K.75, D:R.77, D:K.158

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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