SMTL ID : 9r3i.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 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, G.351, S.353, W.398, R.405, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 14 PLIP interactions: 14 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.434, A:G.436, A:Y.437 Water bridges: A:R.405 Salt bridges: A:R.405 FBP.2: 16 residues within 4Å: Chain B: 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 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.348, B:T.349, B:T.349, B:T.350, B:G.351, B:R.352, B:S.353, B:G.430, B:G.434, B:G.436, B:Y.437, B:T.438 Water bridges: B:R.405, B:R.405 Salt bridges: B:R.405 FBP.4: 17 residues within 4Å: Chain C: 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 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.348, C:T.349, C:T.349, C:T.350, C:T.350, C:G.351, C:R.352, C:S.353, C:G.430, C:G.434, C:G.436, C:Y.437, C:Y.437, C:T.438, C:T.438 Salt bridges: C:R.405 FBP.5: 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.349, D:T.349, D:T.350, D:G.351, D:R.352, D:S.353, D:S.353, D:G.430, D:G.434, D:G.436, D:Y.437, D:T.438 Salt bridges: D:R.405

2 x 01: 4-[4-[[7-(dimethylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl]piperazin-1-yl]sulfonyl-5-pyridin-3-yl-benzene-1,2-diol

01.3: 21 residues within 4Å: Chain A: F.40, L.41, 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, A.304, V.305, Y.306, Q.309, L.310, E.313 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.310 Hydrogen bonds: C:Y.306, C:E.313, A:Q.309, A:E.313 pi-Stacking: C:F.40, C:F.40, A:F.40 pi-Cation interactions: C:F.40, A:F.40 01.6: 21 residues within 4Å: Chain B: F.40, L.41, L.44, L.269, D.270, A.304, V.305, Y.306, Q.309, L.310, E.313 Chain D: F.40, L.41, N.234, L.269, D.270, G.271, Y.306, Q.309, L.310, E.313 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:V.305, B:L.310 Hydrogen bonds: B:E.313, B:E.313, D:Q.309 pi-Stacking: B:F.40, B:F.40, D:F.40 pi-Cation interactions: B:F.40, 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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