SMTL ID : 9r3l.2 (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: 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.209, A:G.211, A:D.212 Salt bridges: A:K.186, A:K.186 OXL.4: 5 residues within 4Å: Chain B: R.87, K.186, E.188, A.209, D.212 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.87, B:E.188, B:G.211, B:D.212, B:D.212 Salt bridges: B:K.186, B:K.186 OXL.6: 8 residues within 4Å: Chain C: K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.211, C:D.212, C:T.244 Salt bridges: C:K.186, C:K.186 OXL.12: 9 residues within 4Å: Chain D: R.87, E.188, M.207, A.209, R.210, D.212, T.244, M.276, S.278 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.212, D:S.278 Salt bridges: D:R.87, D:K.186, D:K.186

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

FBP.2: 19 residues within 4Å: Chain A: L.347, T.348, T.349, T.350, 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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.348, A:T.349, A:T.349, A:T.350, A:G.351, A:R.352, A:S.353, A:S.353, A:G.430, A:G.430, A:G.434, A:S.435, A:G.436, A:Y.437 Water bridges: A:R.405, A:T.438 Salt bridges: A:R.405 FBP.5: 18 residues within 4Å: Chain B: 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 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:L.347, B:L.347, B:T.348, B:T.348, B:T.349, B:T.349, B:T.350, B:G.351, B:S.353, B:S.353, B:G.434, B:G.434, B:G.436, B:Y.437 Water bridges: B:R.405 Salt bridges: B:R.405 FBP.8: 17 residues within 4Å: Chain C: L.347, T.348, T.349, T.350, 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.349, C:T.349, C:T.350, C:S.353, C:S.353, C:G.430, C:G.434, C:G.434, C:G.434, C:G.436, C:Y.437 Water bridges: C:R.405, C:R.405 Salt bridges: C:R.405 FBP.13: 17 residues within 4Å: Chain D: L.347, T.348, T.349, T.350, 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 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:L.347, D:T.348, D:T.349, D:T.349, D:T.350, D:G.351, D:R.352, D:S.353, D:R.405, D:G.430, D:G.434, D:G.434, D:G.436, D:Y.437 Salt bridges: D:R.405

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.186, E.188, D.212 Ligands: OXL.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.188, A:D.212 MG.9: 3 residues within 4Å: Chain C: E.188, D.212 Ligands: OXL.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.212

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

01.7: 21 residues within 4Å: Chain A: F.40, L.41, L.44, L.269, D.270, Y.306, Q.309, L.310, E.313 Chain C: F.40, L.41, L.44, 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 A, 4 interactions with chain C Hydrophobic interactions: A:L.41, A:L.44, A:Q.309, A:L.310, C:N.234 Hydrogen bonds: A:D.270, C:E.313 pi-Stacking: A:F.40, C:F.40 pi-Cation interactions: A:F.40, C:F.40 01.11: 21 residues within 4Å: Chain B: F.40, L.41, L.44, N.234, L.269, D.270, Y.306, Q.309, L.310, E.313 Chain D: F.40, L.41, L.44, G.231, N.234, L.269, D.270, Y.306, Q.309, L.310, E.313 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:Q.309, D:L.310, B:L.41, B:L.44 pi-Stacking: D:F.40, B:F.40, B:F.40 pi-Cation interactions: D:F.40, B:F.40

1 x K: POTASSIUM ION(Non-covalent)

K.10: 5 residues within 4Å: Chain C: N.89, S.91, D.127, T.128, K.129 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.91, C:T.128

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
B

B
D

C
F

D
H

Isoform L-type of Pyruvate kinase PKLR

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