SMTL ID : 9r3m.1 (1 other biounit)

Structure of liver pyruvate kinase in complex with fluorescent probe 8a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 16 residues within 4Å: Chain A: L.347, T.348, T.349, T.350, R.352, S.353, W.398, R.405, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:T.348, A:T.348, A:T.349, A:T.350, A:G.351, A:S.353, A:S.353, A:G.430, A:R.432, A:G.434, A:G.436, A:Y.437 Water bridges: A:T.349, A:T.349, A:R.371, A:R.371, A:R.405, A:R.405, A:R.405, A:T.438 Salt bridges: A:R.405 FBP.6: 17 residues within 4Å: Chain B: L.347, T.348, T.349, T.350, G.351, R.352, S.353, W.398, R.405, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:T.348, B:T.349, B:T.349, B:T.350, B:G.351, B:S.353, B:G.430, B:R.432, B:R.432, B:G.434, B:S.435, B:G.436, B:Y.437 Water bridges: B:R.371, B:R.405, B:R.405, B:G.430, B:T.438 Salt bridges: B:R.405 FBP.10: 16 residues within 4Å: Chain C: L.347, T.348, T.349, T.350, R.352, S.353, W.398, R.405, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:T.348, C:T.348, C:T.349, C:T.349, C:T.350, C:G.351, C:S.353, C:S.353, C:G.430, C:R.432, C:G.434, C:G.436, C:Y.437 Water bridges: C:L.347, C:R.405, C:R.405, C:T.438 Salt bridges: C:R.405 FBP.14: 16 residues within 4Å: Chain D: L.347, T.348, T.349, T.350, R.352, S.353, W.398, R.405, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:T.349, D:T.350, D:G.351, D:S.353, D:S.353, D:G.430, D:R.432, D:R.432, D:G.434, D:S.435, D:G.436, D:Y.437 Water bridges: D:L.347, D:T.349, D:T.349, D:W.398, D:D.401, D:R.405, D:R.405, D:R.405, D:G.430, D:T.438 Salt bridges: D:R.405

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 9 residues within 4Å: Chain A: R.87, K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.211, A:D.212, A:T.244, A:T.244, A:T.244 Water bridges: A:K.186 Salt bridges: A:R.87, A:K.186, A:K.186 OXL.7: 8 residues within 4Å: Chain B: K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.211, B:D.212, B:D.212, B:D.212 Salt bridges: B:R.87, B:K.186 OXL.11: 9 residues within 4Å: Chain C: R.87, K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.211, C:D.212, C:T.244, C:T.244 Water bridges: C:R.87, C:K.186, C:K.186 Salt bridges: C:R.87, C:K.186, C:K.186 OXL.15: 9 residues within 4Å: Chain D: R.87, K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.16 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:E.188, D:G.211, D:D.212, D:D.212, D:T.244, D:T.244, D:T.244 Water bridges: D:R.87, D:R.87, D:K.186 Salt bridges: D:R.87, D:K.186

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.188, D.212 Ligands: OXL.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.188, A:D.212, H2O.2 MG.8: 3 residues within 4Å: Chain B: E.188, D.212 Ligands: OXL.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.188, B:D.212, H2O.8 MG.12: 3 residues within 4Å: Chain C: E.188, D.212 Ligands: OXL.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.188, C:D.212, H2O.14, H2O.14 MG.16: 3 residues within 4Å: Chain D: E.188, D.212 Ligands: OXL.15 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.188, D:D.212, H2O.26, H2O.26

4 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: N.89, S.91, D.127, T.128, S.159, K.186 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.91, A:D.127, A:T.128 K.9: 5 residues within 4Å: Chain B: N.89, S.91, D.127, T.128, S.159 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.91, B:D.127, B:T.128, H2O.13 K.13: 4 residues within 4Å: Chain C: N.89, S.91, D.127, T.128 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.91, C:D.127, C:T.128 K.17: 6 residues within 4Å: Chain D: N.89, S.91, D.127, T.128, S.159, K.186 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.91, D:D.127, D:T.128, H2O.27, H2O.34

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

01.5: 22 residues within 4Å: Chain A: F.40, L.41, L.44, I.230, G.231, N.234, L.269, D.270, G.271, Y.306, Q.309, L.310, E.313 Chain C: F.40, L.41, L.44, L.269, D.270, Y.306, Q.309, L.310, E.313 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:F.40, C:L.41, C:L.44, A:N.234 Hydrogen bonds: C:E.313, C:E.313, A:L.41, A:E.313 pi-Cation interactions: C:F.40, A:F.40 pi-Stacking: A:F.40 01.18: 22 residues within 4Å: Chain B: F.40, L.41, L.44, L.269, D.270, Y.306, Q.309, L.310, E.313 Chain D: F.40, L.41, L.44, I.230, G.231, N.234, L.269, D.270, G.271, Y.306, Q.309, L.310, E.313 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:F.40, B:L.41, B:L.44, B:L.310, D:N.234 Hydrogen bonds: B:D.270 Water bridges: B:Y.306, D:Y.306 pi-Cation interactions: B:F.40, D:F.40 pi-Stacking: D:F.40

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
B

C
C

D
D

Isoform L-type of Pyruvate kinase PKLR

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