SMTL ID : 6ksh.1

Crystal structure of pyruvate kinase (PYK) from Plasmodium falciparum in complex with oxalate and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 5 residues within 4Å: Chain A: K.258, E.260, D.284 Ligands: ATP.3, OXL.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.260, A:D.284, H2O.3 MG.2: 2 residues within 4Å: Ligands: ATP.3, OXL.5 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain B: K.258, E.260, D.284 Ligands: ATP.8, OXL.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.260, B:D.284, H2O.14 MG.7: 2 residues within 4Å: Chain B: S.350 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain C: N.195, E.260, D.284 Ligands: ATP.13, OXL.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.260, C:D.284, H2O.20 MG.12: 2 residues within 4Å: Chain C: S.350 Ligands: ATP.13 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain D: E.260, D.284 Ligands: ATP.18, OXL.20 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.260, D:D.284, H2O.27 MG.17: 3 residues within 4Å: Chain D: T.316, S.350 Ligands: ATP.18 No protein-ligand interaction detected (PLIP)

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

ATP.3: 21 residues within 4Å: Chain A: T.47, L.48, P.50, R.70, N.72, H.75, G.76, H.81, D.105, R.112, K.194, N.195, K.258, D.284, S.350, G.351, A.354 Ligands: MG.1, MG.2, K.4, OXL.5 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:L.48, A:N.72, A:D.105, A:K.194, A:N.195 Water bridges: A:R.70, A:R.70, A:R.112, A:D.165, A:D.165, A:K.194, A:K.194, A:S.231, A:K.258, A:K.258, A:S.350, A:S.350, A:G.351 Salt bridges: A:R.70, A:R.70, A:H.75, A:H.75, A:R.112, A:R.112, A:K.258 pi-Stacking: A:H.75 ATP.8: 21 residues within 4Å: Chain B: T.47, L.48, P.50, R.70, N.72, H.75, G.76, H.81, D.105, R.112, K.194, N.195, K.258, D.284, S.350, G.351, A.354 Ligands: MG.6, MG.7, K.9, OXL.10 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:L.48, B:N.72, B:D.105, B:D.165, B:K.194, B:N.195, B:S.350 Water bridges: B:R.112, B:K.194, B:K.194, B:K.194, B:N.195, B:K.258, B:K.258, B:G.351 Salt bridges: B:R.70, B:R.70, B:H.75, B:H.75, B:R.112, B:R.112, B:K.258 pi-Stacking: B:H.75 ATP.13: 20 residues within 4Å: Chain C: T.47, L.48, P.50, R.70, N.72, H.75, G.76, H.81, R.112, K.194, N.195, K.258, D.284, S.350, G.351, A.354 Ligands: MG.11, MG.12, K.14, OXL.15 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:L.48, C:N.72, C:K.194, C:N.195, C:S.350 Water bridges: C:R.70, C:R.70, C:D.165, C:D.165, C:K.194, C:N.195, C:S.231, C:K.258, C:K.258 Salt bridges: C:R.70, C:R.70, C:H.75, C:H.75, C:R.112, C:R.112, C:K.258 pi-Stacking: C:H.75 ATP.18: 20 residues within 4Å: Chain D: T.47, L.48, P.50, R.70, N.72, H.75, H.81, D.105, R.112, K.194, N.195, K.258, D.284, S.350, G.351, A.354 Ligands: MG.16, MG.17, K.19, OXL.20 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:L.48, D:N.72, D:K.194, D:N.195 Water bridges: D:R.70, D:R.70, D:R.112, D:D.165, D:K.194, D:K.194, D:K.194, D:N.195, D:S.231, D:K.258, D:K.258, D:G.351 Salt bridges: D:R.70, D:R.70, D:H.75, D:H.75, D:R.112, D:R.112, D:K.258 pi-Stacking: D:H.75

4 x K: POTASSIUM ION(Non-covalent)

K.4: 7 residues within 4Å: Chain A: N.72, S.74, D.105, T.106, S.231, K.258 Ligands: ATP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.74, A:D.105, A:T.106, H2O.1 K.9: 7 residues within 4Å: Chain B: N.72, S.74, D.105, T.106, S.231, K.258 Ligands: ATP.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.74, B:D.105, B:T.106 K.14: 6 residues within 4Å: Chain C: N.72, S.74, D.105, T.106, S.231 Ligands: ATP.13 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.74, C:D.105, C:T.106, H2O.19 K.19: 7 residues within 4Å: Chain D: N.72, S.74, D.105, T.106, S.231, K.258 Ligands: ATP.18 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.74, D:D.105, D:T.106, H2O.28

4 x OXL: OXALATE ION(Non-covalent)

OXL.5: 12 residues within 4Å: Chain A: R.70, K.258, E.260, A.281, R.282, G.283, D.284, T.316, M.348 Ligands: MG.1, MG.2, ATP.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.260, A:G.283, A:D.284, A:T.316 Water bridges: A:R.70, A:N.195, A:K.258 Salt bridges: A:R.70, A:K.258 OXL.10: 11 residues within 4Å: Chain B: R.70, K.258, E.260, A.281, R.282, G.283, D.284, T.316, M.348 Ligands: MG.6, ATP.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.260, B:G.283, B:D.284, B:D.284 Water bridges: B:N.195, B:K.258 Salt bridges: B:R.70, B:K.258 OXL.15: 10 residues within 4Å: Chain C: R.70, K.258, E.260, A.281, R.282, G.283, D.284, T.316 Ligands: MG.11, ATP.13 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.283, C:D.284, C:T.316, C:T.316, C:T.316 Water bridges: C:R.70, C:N.195, C:N.195, C:K.258 Salt bridges: C:R.70, C:K.258, C:K.258 OXL.20: 11 residues within 4Å: Chain D: R.70, K.258, E.260, A.281, R.282, G.283, D.284, T.316, M.348 Ligands: MG.16, ATP.18 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.283, D:D.284, D:T.316, D:T.316 Water bridges: D:R.70, D:R.70, D:N.195, D:K.258, D:K.258 Salt bridges: D:R.70, D:K.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, W. et al., Pyruvate kinase from Plasmodium falciparum: Structural and kinetic insights into the allosteric mechanism. Biochem.Biophys.Res.Commun. (2020)

Release Date

2020-08-26

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase