SMTL ID : 9r3l.1 (1 other biounit)

Structure of liver pyruvate kinase in complex with fluorescent probe 4d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-tetramer

Ligands

4 x OXL: OXALATE ION(Non-covalent)

OXL.1: 8 residues within 4Å: Chain A: R.87, K.186, E.188, A.209, G.211, D.212, T.244 Ligands: MG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.87, A:G.211, A:D.212, A:T.244 Salt bridges: A:K.186, A:K.186 OXL.6: 9 residues within 4Å: Chain B: R.87, K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.211, B:D.212, B:T.244, B:T.244 Salt bridges: B:R.87, B:K.186, B:K.186 OXL.12: 10 residues within 4Å: Chain C: R.87, K.186, E.188, A.209, R.210, G.211, D.212, T.244, M.276 Ligands: MG.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.211, C:D.212, C:T.244 Salt bridges: C:R.87, C:K.186, C:K.186 OXL.16: 9 residues within 4Å: Chain D: K.186, E.188, M.207, A.209, R.210, G.211, D.212, T.244 Ligands: MG.18 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.188, D:G.211, D:D.212, D:T.244, D:T.244 Salt bridges: D:R.87, D:K.186

2 x 01: 4-[4-[[7-(azetidin-1-yl)-2,1,3-benzoxadiazol-4-yl]sulfonyl]piperazin-1-yl]sulfonylbenzene-1,2-diol

01.2: 21 residues within 4Å: Chain A: F.40, L.41, L.44, N.234, L.269, D.270, Y.306, Q.309, L.310, E.313, L.314 Chain C: F.40, L.41, L.44, N.234, L.269, D.270, Y.306, Q.309, L.310, E.313 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:Q.309, A:L.314, C:L.41, C:L.310 pi-Stacking: A:F.40, C:F.40, C:F.40 pi-Cation interactions: A:F.40, C:F.40 Hydrogen bonds: C:N.234, C:E.313 01.15: 20 residues within 4Å: Chain B: F.40, L.41, L.44, G.231, N.234, L.269, D.270, Y.306, Q.309, L.310, E.313 Chain D: F.40, L.41, L.44, L.269, D.270, Y.306, Q.309, L.310, E.313 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:N.234, D:L.41, D:L.310 pi-Stacking: B:F.40, D:F.40, D:F.40 pi-Cation interactions: B:F.40, D:F.40

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

FBP.3: 18 residues within 4Å: Chain A: L.347, T.348, T.349, T.350, G.351, R.352, S.353, W.398, R.405, T.429, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.349, A:T.349, A:T.349, A:T.350, A:T.350, A:G.351, A:R.352, A:S.353, A:S.353, A:G.430, A:G.434, A:G.434, A:G.434, A:G.436, A:Y.437, A:T.438 Water bridges: A:R.405 Salt bridges: A:R.405 FBP.7: 20 residues within 4Å: Chain B: L.347, T.348, T.349, T.350, G.351, R.352, S.353, W.398, V.402, R.405, T.429, G.430, W.431, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.349, B:T.349, B:T.350, B:G.351, B:S.353, B:G.430, B:R.432, B:G.434, B:G.434, B:G.434, B:G.436, B:Y.437 Water bridges: B:R.371 Salt bridges: B:R.405 FBP.13: 18 residues within 4Å: Chain C: L.347, T.348, T.349, T.350, G.351, R.352, S.353, W.398, R.405, T.429, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.348, C:T.348, C:T.349, C:T.349, C:T.349, C:T.350, C:G.351, C:S.353, C:S.353, C:G.430, C:G.434, C:G.436, C:T.438 Salt bridges: C:R.405 FBP.17: 18 residues within 4Å: Chain D: L.347, T.348, T.349, T.350, G.351, R.352, S.353, W.398, R.405, T.429, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.348, D:T.348, D:T.349, D:T.349, D:T.350, D:G.351, D:S.353, D:G.430, D:G.430, D:G.434, D:G.436, D:Y.437 Water bridges: D:R.352 Salt bridges: D:R.405

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

MG.4: 5 residues within 4Å: Chain A: S.159, K.186, E.188, D.212 Ligands: OXL.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.188, A:E.188, A:D.212, H2O.4 MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: K.186, E.188, D.212 Ligands: OXL.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.188, B:D.212, H2O.7 MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain C: K.186, E.188, D.212 Ligands: OXL.12 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.188, C:D.212 MG.18: 4 residues within 4Å: Chain D: K.186, E.188, D.212 Ligands: OXL.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.188, D:D.212

3 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.11: 6 residues within 4Å: Chain B: N.89, S.91, D.127, T.128, S.159, K.186 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.127, B:T.128 K.19: 6 residues within 4Å: Chain D: N.89, S.91, D.127, T.128, S.159, K.186 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nilsson, O. et al., Fluorescent binding assay for allosteric ligands of liver pyruvate kinase. Eur.J.Med.Chem. (2025)

Release Date

2025-08-13

Peptides

Isoform L-type of Pyruvate kinase PKLR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

Isoform L-type of Pyruvate kinase PKLR

Related Entries With Identical Sequence