SMTL ID : 4ks0.1

Pyruvate kinase (PYK) from Trypanosoma cruzi in the presence of Magnesium, oxalate and F26BP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.259, E.261, D.285 Ligands: OXL.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.261, A:D.285, H2O.5, H2O.5 MG.5: 4 residues within 4Å: Chain B: K.259, E.261, D.285 Ligands: OXL.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.261, B:D.285, H2O.10, H2O.10 MG.9: 4 residues within 4Å: Chain C: K.259, E.261, D.285 Ligands: OXL.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.261, C:D.285, H2O.15, H2O.15 MG.13: 4 residues within 4Å: Chain D: K.259, E.261, D.285 Ligands: OXL.15 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.261, D:D.285, H2O.20, H2O.20

4 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: N.72, S.74, D.104, T.105, S.232, K.259 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.74, A:D.104, A:T.105, H2O.5 K.6: 5 residues within 4Å: Chain B: N.72, S.74, D.104, T.105, S.232 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.104, B:T.105, H2O.10 K.10: 6 residues within 4Å: Chain C: N.72, S.74, D.104, T.105, S.232, K.259 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.74, C:D.104, C:T.105, H2O.15 K.14: 5 residues within 4Å: Chain D: N.72, S.74, D.104, T.105, S.232 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.104, D:T.105, H2O.20

4 x OXL: OXALATE ION(Non-covalent)

OXL.3: 8 residues within 4Å: Chain A: K.259, E.261, A.282, R.283, G.284, D.285, T.317 Ligands: MG.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.284, A:D.285, A:T.317 Water bridges: A:K.259 Salt bridges: A:R.70, A:K.259 OXL.7: 8 residues within 4Å: Chain B: K.259, E.261, A.282, R.283, G.284, D.285, T.317 Ligands: MG.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.284, B:D.285, B:D.285, B:T.317, B:T.317 Water bridges: B:R.70 Salt bridges: B:R.70, B:K.259, B:K.259 OXL.11: 8 residues within 4Å: Chain C: K.259, E.261, A.282, R.283, G.284, D.285, T.317 Ligands: MG.9 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.284, C:D.285, C:D.285, C:T.317, C:T.317 Water bridges: C:K.259 Salt bridges: C:R.70, C:K.259 OXL.15: 8 residues within 4Å: Chain D: K.259, E.261, A.282, R.283, G.284, D.285, T.317 Ligands: MG.13 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.284, D:D.285, D:T.317 Water bridges: D:R.70 Salt bridges: D:R.70, D:K.259, D:K.259

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

FDP.4: 15 residues within 4Å: Chain A: L.420, S.421, N.422, S.423, R.425, S.426, K.474, R.477, H.501, A.502, V.506, K.507, G.508, Y.509, P.510 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.421, A:N.422, A:N.422, A:S.423, A:S.426, A:S.426, A:K.474, A:A.502, A:V.506, A:G.508 Water bridges: A:K.474, A:K.474, A:R.477, A:R.477 Salt bridges: A:K.474, A:R.477 FDP.8: 15 residues within 4Å: Chain B: L.420, S.421, N.422, S.423, R.425, S.426, K.474, R.477, H.501, A.502, V.506, K.507, G.508, Y.509, P.510 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.421, B:N.422, B:N.422, B:S.423, B:G.424, B:S.426, B:S.426, B:S.426, B:K.474, B:A.502, B:G.508, B:Y.509 Water bridges: B:N.422, B:S.423 Salt bridges: B:K.474, B:R.477 FDP.12: 15 residues within 4Å: Chain C: L.420, S.421, N.422, S.423, R.425, S.426, K.474, R.477, H.501, A.502, V.506, K.507, G.508, Y.509, P.510 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.421, C:N.422, C:N.422, C:S.423, C:S.426, C:S.426, C:K.474, C:A.502, C:V.506, C:G.508 Water bridges: C:K.474, C:K.474, C:R.477, C:R.477 Salt bridges: C:K.474, C:R.477 FDP.16: 15 residues within 4Å: Chain D: L.420, S.421, N.422, S.423, R.425, S.426, K.474, R.477, H.501, A.502, V.506, K.507, G.508, Y.509, P.510 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.421, D:N.422, D:N.422, D:S.423, D:G.424, D:S.426, D:S.426, D:S.426, D:K.474, D:A.502, D:G.508, D:Y.509 Water bridges: D:N.422, D:S.423 Salt bridges: D:K.474, D:R.477

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H.P. et al., Structures of pyruvate kinases display evolutionarily divergent allosteric strategies. R Soc Open Sci (2014)

Release Date

2014-11-19

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate kinase

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