SMTL ID : 3hqp.4 (15 other biounits)

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.146, S.331 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: K.239, E.241, D.265 Ligands: OXL.4, ATP.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.241, A:D.265, H2O.9

2 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: N.52, S.54, D.84, T.85, S.212, K.239 Ligands: ATP.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.54, A:D.84, A:T.85, H2O.1 K.7: 4 residues within 4Å: Chain A: Q.355, S.356, L.358, E.360 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Q.355, A:L.358, A:E.360

1 x OXL: OXALATE ION(Non-covalent)

OXL.4: 11 residues within 4Å: Chain A: R.50, K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297 Ligands: MG.2, ATP.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.241, A:G.264, A:D.265, A:T.297, A:T.297 Water bridges: A:K.239, A:K.239 Salt bridges: A:R.50, A:K.239, A:K.239

1 x FDP: 2,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FDP.5: 15 residues within 4Å: Chain A: L.400, S.401, N.402, T.403, R.405, S.406, K.454, R.457, H.481, A.482, V.486, K.487, G.488, Y.489, A.490 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.401, A:N.402, A:N.402, A:T.403, A:G.404, A:R.405, A:S.406, A:K.454, A:A.482, A:V.486, A:G.488 Water bridges: A:R.405, A:R.405, A:K.454, A:K.454 Salt bridges: A:R.405, A:K.454, A:R.457

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

ATP.6: 21 residues within 4Å: Chain A: T.27, I.28, P.30, R.50, N.52, H.55, Y.60, H.61, D.84, R.91, R.176, K.239, D.265, S.331, G.332, A.335, K.336 Ligands: MG.1, MG.2, K.3, OXL.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:T.27, A:I.28, A:N.52, A:H.55, A:D.84, A:R.176, A:R.176, A:S.331, A:K.336 Water bridges: A:D.146, A:G.177, A:S.212, A:S.212, A:K.239, A:K.239, A:T.297, A:T.297, A:G.332 Salt bridges: A:R.50, A:R.50, A:H.55, A:R.91, A:R.91, A:K.239 pi-Cation interactions: A: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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Pyruvate kinase

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