SMTL ID : 5ws9.1

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, ATP and allosteric activator AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: 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.5, H2O.8 MG.7: 3 residues within 4Å: Chain B: 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.20, H2O.23 MG.13: 3 residues within 4Å: Chain C: E.223, D.247 Ligands: OXL.15 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.223, C:D.247, H2O.32, H2O.34 MG.14: 3 residues within 4Å: Chain C: D.129, T.279 Ligands: ATP.17 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain D: E.223, D.247 Ligands: OXL.21 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.223, D:D.247, H2O.45, H2O.46 MG.20: 2 residues within 4Å: Chain D: D.129 Ligands: ATP.24 No protein-ligand interaction detected (PLIP)

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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.246, A:D.247, A:T.279, A:T.279 Water bridges: A:K.221 Salt bridges: A:R.36, 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:G.246, B:D.247, B:T.279 Water bridges: B:R.36, B:K.221, B:E.223 Salt bridges: B:R.36, B:K.221 OXL.15: 9 residues within 4Å: Chain C: K.221, E.223, A.244, R.245, G.246, D.247, T.279, M.311 Ligands: MG.13 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.246, C:D.247, C:T.279 Water bridges: C:R.36, C:K.221, C:E.223 Salt bridges: C:R.36, C:K.221 OXL.21: 9 residues within 4Å: Chain D: K.221, E.223, A.244, R.245, G.246, D.247, T.279, M.311 Ligands: MG.19 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.246, D:D.247, D:T.279, D:T.279 Water bridges: D:R.36, D:K.221 Salt bridges: D:R.36, D:K.221

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 26 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:T.377, A:T.377, A:Q.378, A:S.379, A:G.380, A:T.382, A:P.420, A:M.422, A:G.453, A:G.457, A:T.458, A:G.460, A:S.461, A:S.461, A:T.462, A:T.462 Salt bridges: A:R.354 pi-Stacking: A:W.401 AMP.9: 26 residues within 4Å: Chain B: 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 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:T.377, B:Q.378, B:S.379, B:S.379, B:G.380, B:D.381, B:T.382, B:T.382, B:A.400, B:P.420, B:M.422, B:G.453, B:G.457, B:T.458, B:G.460, B:S.461, B:S.461, B:T.462 Water bridges: B:R.354 Salt bridges: B:R.354 pi-Stacking: B:W.401 AMP.16: 26 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:T.377, C:Q.378, C:S.379, C:G.380, C:D.381, C:T.382, 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, C:T.462 Salt bridges: C:R.354 pi-Stacking: C:W.401 AMP.22: 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 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.378, D:S.379, D:S.379, D:G.380, D:D.381, D:T.382, D:T.382, D:P.420, D:M.422, D:G.453, D:G.457, D:T.458, D:G.460, D:S.461, D:T.462 Salt bridges: D:R.354 pi-Stacking: D:W.401

3 x K: POTASSIUM ION(Non-covalent)

K.4: 7 residues within 4Å: Chain A: N.38, S.40, D.70, L.71, Q.72, S.194, K.221 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.70 K.10: 7 residues within 4Å: Chain B: N.38, S.40, D.70, L.71, Q.72, S.194, K.221 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.70, H2O.19, H2O.26 K.23: 7 residues within 4Å: Chain D: N.38, S.40, D.70, L.71, Q.72, S.194, K.221 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.70, H2O.49

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 9 residues within 4Å: Chain A: P.16, R.36, N.38, S.40, H.41, S.313, G.314, S.317, V.318 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.38, A:S.40, A:G.314, A:S.317 Water bridges: A:L.14, A:R.36, A:R.36, A:R.36, A:R.36, A:H.41, A:Q.280, A:S.313, A:S.313 Salt bridges: A:R.36, A:H.41 pi-Stacking: A:H.41, A:H.41 ATP.11: 9 residues within 4Å: Chain B: P.16, R.36, N.38, S.40, H.41, S.313, G.314, S.317, V.318 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.38, B:G.314, B:S.317 Water bridges: B:L.14, B:R.36, B:R.36, B:R.36, B:R.36, B:H.41, B:S.313, B:S.313, B:S.313, B:E.315 Salt bridges: B:R.36, B:H.41 pi-Stacking: B:H.41, B:H.41 ATP.17: 13 residues within 4Å: Chain C: T.13, P.16, R.36, N.38, H.41, R.77, D.128, K.158, S.313, G.314, S.317, V.318 Ligands: MG.14 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:N.38, C:S.40, C:R.77, C:D.128, C:K.158, C:G.314, C:S.317 Water bridges: C:R.36, C:R.36, C:R.77, C:D.128, C:D.129, C:S.313 Salt bridges: C:R.36, C:H.41 pi-Stacking: C:H.41, C:H.41 ATP.24: 13 residues within 4Å: Chain D: T.13, P.16, R.36, N.38, S.40, H.41, R.77, D.128, S.313, G.314, S.317, V.318 Ligands: MG.20 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:N.38, D:S.40, D:S.40, D:R.77, D:D.128, D:G.314, D:S.317 Water bridges: D:R.36, D:R.36, D:K.131, D:Q.280, D:S.313, D:S.313, D:E.315 Salt bridges: D:R.36, D:H.41 pi-Stacking: D:H.41, D:H.41

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

PO4.6: 7 residues within 4Å: Chain A: P.350, R.351, T.352, G.355, V.356, R.385, R.388 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.351, A:T.352, A:T.352, A:T.352, A:G.355, A:V.356 Water bridges: A:R.385, A:R.385, A:R.388 Salt bridges: A:R.385, A:R.388 PO4.12: 6 residues within 4Å: Chain B: P.350, R.351, T.352, G.355, R.385, R.388 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.351, B:T.352, B:G.355 Water bridges: B:R.385, B:R.388 Salt bridges: B:R.385, B:R.388 PO4.18: 6 residues within 4Å: Chain C: 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, C:G.355 Water bridges: C:R.385 Salt bridges: C:R.385, C:R.388 PO4.25: 7 residues within 4Å: Chain D: P.350, R.351, T.352, G.355, V.356, R.385, R.388 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.351, D:T.352, D:G.355, D:V.356 Salt bridges: D:R.385, D:R.388

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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