SMTL ID : 3hqo.2 (3 other biounits)

Crystal structures of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP and Oxalate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.146, T.297 Ligands: OXL.4, ATP.5 No protein-ligand interaction detected (PLIP) MG.2: 8 residues within 4Å: Chain A: S.212, F.213, K.239, E.241, D.265 Ligands: K.3, OXL.4, ATP.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.241, A:D.265 MG.6: 4 residues within 4Å: Chain B: D.146, T.297 Ligands: OXL.9, ATP.10 No protein-ligand interaction detected (PLIP) MG.7: 8 residues within 4Å: Chain B: S.212, F.213, K.239, E.241, D.265 Ligands: K.8, OXL.9, ATP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.241, B:D.265

2 x K: POTASSIUM ION(Non-covalent)

K.3: 10 residues within 4Å: Chain A: N.52, S.54, D.84, T.85, E.89, R.91, S.212, K.239 Ligands: MG.2, ATP.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.54, A:T.85 K.8: 10 residues within 4Å: Chain B: N.52, S.54, D.84, T.85, E.89, R.91, S.212, K.239 Ligands: MG.7, ATP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.54, B:T.85

2 x OXL: OXALATE ION(Non-covalent)

OXL.4: 11 residues within 4Å: Chain A: R.50, K.239, E.241, A.262, R.263, G.264, D.265, T.297 Ligands: MG.1, MG.2, ATP.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.241, A:G.264, A:D.265, A:T.297 Salt bridges: A:R.50, A:K.239, A:K.239 OXL.9: 11 residues within 4Å: Chain B: R.50, K.239, E.241, A.262, R.263, G.264, D.265, T.297 Ligands: MG.6, MG.7, ATP.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.264, B:D.265, B:D.265, B:T.297, B:T.297 Salt bridges: B:R.50, B:K.239, B:K.239

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

ATP.5: 19 residues within 4Å: Chain A: T.27, I.28, R.50, N.52, H.55, Y.60, D.84, R.91, D.146, R.176, K.239, D.265, S.331, A.335, K.336 Ligands: MG.1, MG.2, K.3, OXL.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.27, A:I.28, A:N.52, A:D.84, A:G.332, A:K.336 Salt bridges: A:R.50, A:R.50, A:H.55, A:R.91, A:R.91, A:K.239 pi-Stacking: A:H.55, A:H.55 ATP.10: 19 residues within 4Å: Chain B: T.27, I.28, R.50, N.52, H.55, Y.60, D.84, R.91, D.146, R.176, K.239, D.265, S.331, A.335, K.336 Ligands: MG.6, MG.7, K.8, OXL.9 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.27, B:T.27, B:I.28, B:N.52, B:D.84, B:G.332, B:K.336 Salt bridges: B:R.50, B:R.50, B:H.55, B:R.91, B:R.91, B:K.239 pi-Stacking: B:H.55, B:H.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H.P. et al., The allosteric mechanism of pryuvate kinase from Leishmania mexicana: a rock and lock model. J.Biol.Chem. (2010)

Release Date

2010-02-16

Peptides

Pyruvate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyruvate kinase

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