SMTL ID : 6ito.1

Crystal structure of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, AMP and inhibitor Ribose 5-Phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 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.1 MG.5: 4 residues within 4Å: Chain B: K.221, E.223, D.247 Ligands: OXL.6 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.9: 4 residues within 4Å: Chain C: K.221, E.223, D.247 Ligands: OXL.10 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.223, C:D.247, H2O.11, H2O.11 MG.13: 4 residues within 4Å: Chain D: K.221, E.223, D.247 Ligands: OXL.14 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.223, D:D.247, H2O.16, H2O.17

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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.223, A:E.223, A:G.246, A:D.247, A:T.279 Water bridges: A:R.36, A:R.36, A:K.221, A:K.221 Salt bridges: A:R.36, A:K.221, A:K.221 OXL.6: 8 residues within 4Å: Chain B: K.221, E.223, A.244, R.245, G.246, D.247, T.279 Ligands: MG.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.246, B:D.247, B:T.279, B:T.279 Water bridges: B:K.221, B:K.221 Salt bridges: B:R.36, B:K.221 OXL.10: 8 residues within 4Å: Chain C: K.221, E.223, A.244, R.245, G.246, D.247, T.279 Ligands: MG.9 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:E.223, C:E.223, C:G.246, C:D.247, C:T.279 Water bridges: C:R.36, C:K.221, C:K.221 Salt bridges: C:R.36, C:K.221, C:K.221 OXL.14: 8 residues within 4Å: Chain D: K.221, E.223, A.244, R.245, G.246, D.247, T.279 Ligands: MG.13 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.246, D:D.247, D:T.279, D:T.279 Water bridges: D:R.36, D:R.36, D:K.221, D:K.221 Salt bridges: D:R.36, D:K.221, D:K.221

4 x R5P: RIBOSE-5-PHOSPHATE(Non-covalent)

R5P.3: 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.271, A:R.351, A:T.352, A:G.355, A:R.385, A:R.385 Salt bridges: A:H.348, A:R.385, A:R.388 R5P.7: 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 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.271, B:R.351, B:T.352, B:G.355, B:R.385, B:R.385 Salt bridges: B:H.348, B:R.385, B:R.388 R5P.11: 10 residues within 4Å: Chain C: L.236, E.270, N.271, H.348, P.350, R.351, T.352, G.355, R.385, R.388 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.271, C:R.351, C:T.352, C:G.355, C:R.385, C:R.385 Salt bridges: C:H.348, C:R.385, C:R.388 R5P.15: 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 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:E.270, D:N.271, D:R.351, D:T.352, D:T.352, D:G.355, D:R.385, D:R.385 Salt bridges: D:H.348, D:R.385, D:R.388

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 25 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.456, G.457, T.458, V.459, G.460, S.461, T.462 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Q.378, A:S.379, A:S.379, A:G.380, A:D.381, A:T.382, A:T.382, A:A.400, A:P.420, A:M.422, A:G.453, A:G.457, A:G.460, A:S.461 Salt bridges: A:R.354 pi-Stacking: A:W.401, A:W.401 AMP.8: 25 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.456, G.457, T.458, V.459, G.460, S.461, T.462 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.377, B:T.377, B:Q.378, B:S.379, B:G.380, B:D.381, B:T.382, B:P.420, B:M.422, B:G.453, B:G.453, B:G.457, B:G.460, B:S.461 Salt bridges: B:R.354 pi-Stacking: B:W.401, B:W.401 AMP.12: 25 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.456, G.457, T.458, V.459, G.460, S.461, T.462 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:T.377, C:Q.378, C:S.379, C:S.379, C:G.380, C:D.381, C:T.382, C:T.382, C:P.420, C:M.422, C:G.453, C:G.457, C:G.460, C:S.461 Salt bridges: C:R.354 pi-Stacking: C:W.401, C:W.401 AMP.16: 25 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.456, G.457, T.458, V.459, G.460, S.461, T.462 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:T.377, D:T.377, D:Q.378, D:S.379, D:G.380, D:D.381, D:T.382, D:P.420, D:M.422, D:G.453, D:G.453, D:G.457, D:G.460, D:S.461 Salt bridges: D:R.354 pi-Stacking: D:W.401, D:W.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, W. et al., Pyruvate Kinase Regulates the Pentose-Phosphate Pathway in Response to Hypoxia in Mycobacterium tuberculosis. J.Mol.Biol. (2019)

Release Date

2019-08-14

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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