PDB-9r3m: Structure of liver pyruvate kinase in complex with fluorescent pr...

ID or keywords:

Entry

Database: PDB / ID: 9r3m

Title

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

Components

Isoform L-type of Pyruvate kinase PKLR

Keywords

TRANSFERASE / Pyruvate kinase / fluorescence / allosteric site

Function / homology

Function and homology information

pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / response to metal ion / Glycolysis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.062 Å

Authors

Bogucka, A. / Nilsson, O. / Grotli, M. / Hyvonen, M.

Funding support

United Kingdom, 1items

Citation

Journal: Eur.J.Med.Chem. / Year: 2025
Title: Fluorescent binding assay for allosteric ligands of liver pyruvate kinase.
Authors: Nilsson, O. / Bogucka, A. / Koteles, I. / Haversen, L. / Liljenberg, S. / Rutberg, M. / Hyvonen, M. / Grotli, M.

History

Deposition	May 5, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 13, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9r3m.cif.gz	713.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9r3m.ent.gz		Display	PDB format
PDBx/mmJSON format	9r3m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9r3m_validation.pdf.gz	4.3 MB	Display	wwPDB validaton report
Full document	9r3m_full_validation.pdf.gz	4.3 MB	Display
Data in XML	9r3m_validation.xml.gz	165.4 KB	Display
Data in CIF	9r3m_validation.cif.gz	220.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r3/9r3m ftp://data.pdbj.org/pub/pdb/validation_reports/r3/9r3m	HTTPS FTP

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Related structure data

Related structure data	9r3hC 9r3iC 9r3lC 9r3oC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (15) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #14 - Feb 2001 Insulin similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1)

Deposited unit

A: Isoform L-type of Pyruvate kinase PKLR

B: Isoform L-type of Pyruvate kinase PKLR

C: Isoform L-type of Pyruvate kinase PKLR

D: Isoform L-type of Pyruvate kinase PKLR

E: Isoform L-type of Pyruvate kinase PKLR

F: Isoform L-type of Pyruvate kinase PKLR

G: Isoform L-type of Pyruvate kinase PKLR

H: Isoform L-type of Pyruvate kinase PKLR

hetero molecules

392 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Isoform L-type of Pyruvate kinase PKLR

B: Isoform L-type of Pyruvate kinase PKLR

C: Isoform L-type of Pyruvate kinase PKLR

D: Isoform L-type of Pyruvate kinase PKLR

hetero molecules

defined by author&software
Evidence: gel filtration, Stable tetramer
196 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Isoform L-type of Pyruvate kinase PKLR

F: Isoform L-type of Pyruvate kinase PKLR

G: Isoform L-type of Pyruvate kinase PKLR

H: Isoform L-type of Pyruvate kinase PKLR

hetero molecules

defined by author&software
196 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	208.443, 112.896, 189.009
Angle α, β, γ (deg.)	90, 91.06, 90
Int Tables number	5
Space group name H-M	C121

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein

Isoform L-type of Pyruvate kinase PKLR / Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver ...

Mass: 48285.379 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PKLR, PK1, PKL / Production host:

Escherichia coli (E. coli) / References: UniProt: P30613, pyruvate kinase

#2: Sugar

ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose

Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₂P₂

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Non-polymers , 5 types, 2136 molecules

#3: Chemical	ChemComp-OXL / OXALATE ION Mass: 88.019 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂O₄
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Chemical	ChemComp-A1JBZ / 4-[4-[(7-piperidin-1-yl-2,1,3-benzoxadiazol-4-yl)sulfonyl]piperazin-1-yl]sulfonylbenzene-1,2-diol / ISODZKPLYYJZLI-UHFFFAOYSA-N Mass: 523.582 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₅N₅O₇S₂ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2108 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.26 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES/MOPS, 10% PEG8000, 20% ethylene glycol, 10 mM phenylalanine, 20 mM sodium oxalate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.97629 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 20, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97629 Å / Relative weight: 1

Reflection

Resolution: 2.062→104.204 Å / Num. obs: 184428 / % possible obs: 91.3 % / Redundancy: 7.11 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC_1/2: 0.998 / CC_1/2 anomalous: -0.063 / R_merge(I) obs: 0.1266 / R_pim(I) all: 0.0507 / R_rim(I) all: 0.1366 / AbsDiff over sigma anomalous: 0.753 / B_aniso tensor eigenvalue 1: 0 Å² / B_aniso tensor eigenvalue 2: 15.372 Å² / B_aniso tensor eigenvalue 3: 24.6189 Å² / B_aniso tensor eigenvector 1 ortho1: 0.7122 / B_aniso tensor eigenvector 1 ortho2: 0 / B_aniso tensor eigenvector 1 ortho3: -0.702 / B_aniso tensor eigenvector 2 ortho1: 0 / B_aniso tensor eigenvector 2 ortho2: 1 / B_aniso tensor eigenvector 2 ortho3: 0 / B_aniso tensor eigenvector 3 ortho1: 0.702 / B_aniso tensor eigenvector 3 ortho2: 0 / B_aniso tensor eigenvector 3 ortho3: 0.7122 / Aniso diffraction limit 1: 2.057 Å / Aniso diffraction limit 2: 2.435 Å / Aniso diffraction limit 3: 2.363 Å / Aniso diffraction limit axis 1 ortho1: 0.77918 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: -0.62678 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0.62678 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.77918 / Net I/σ(I): 9.89 / Num. measured all: 1310724 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 91.2 / % possible ellipsoidal: 91.3 / % possible ellipsoidal anomalous: 91.2 / % possible spherical: 68.5 / % possible spherical anomalous: 68.1 / Redundancy anomalous: 3.62 / Signal type: local

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. measured obs	Num. unique all	Num. unique obs	CC_1/2	CC_1/2 anomalous	R_pim(I) all	R_rim(I) all	AbsDiff over sigma anomalous	% possible anomalous	% possible ellipsoidal	% possible ellipsoidal anomalous	% possible spherical	% possible spherical anomalous	Redundancy anomalous	% possible all
6.411-104.204	7.38	0.0384	31.26	68094	68094	9221	9221	0.999	-0.131	0.0151	0.0413	0.731	99.8	100	99.8	100	99.8	3.86	100
5.074-6.411	6.49	0.0604	21.9	59858	59858	9222	9222	0.998	-0.129	0.0257	0.0658	0.809	100	100	100	100	100	3.32	100
4.424-5.074	7.18	0.0547	25.89	66226	66226	9221	9221	0.998	-0.107	0.0218	0.0589	0.804	100	99.9	100	99.9	100	3.66	99.9
4.016-4.424	7.37	0.0649	23.24	67966	67966	9222	9222	0.998	-0.111	0.0255	0.0698	0.806	100	99.8	100	99.8	100	3.75	99.8
3.697-4.016	7.21	0.0801	19.15	66513	66513	9221	9221	0.997	-0.092	0.0318	0.0863	0.773	89	89.6	89	89.6	89	3.69	89.6
3.411-3.697	6.82	0.1042	14.6	62918	62918	9221	9221	0.995	-0.071	0.0423	0.1127	0.8	70.1	72	70.1	72	70.1	3.54	72
3.25-3.411	7.43	0.1406	11.64	68475	68475	9222	9222	0.993	-0.051	0.0549	0.151	0.772	99.5	99.7	99.5	99.7	99.5	3.77	99.7
3.116-3.25	6.69	0.1778	8.74	61684	61684	9221	9221	0.986	-0.057	0.0744	0.1931	0.762	99.2	99.6	99.2	99.6	99.2	3.4	99.6
3.002-3.116	6.33	0.2213	6.9	58357	58357	9222	9222	0.978	-0.012	0.0965	0.242	0.756	99.6	99.6	99.6	99.6	99.6	3.21	99.6
2.903-3.002	6.83	0.2702	6.03	62962	62962	9221	9221	0.975	-0.039	0.1114	0.2926	0.743	99.7	99.5	99.7	99.5	99.7	3.45	99.5
2.815-2.903	7.02	0.3454	4.88	64725	64725	9221	9221	0.965	-0.015	0.1395	0.3728	0.742	99.7	99.5	99.7	99.5	99.7	3.55	99.5
2.737-2.815	7.11	0.3989	4.29	65591	65591	9222	9222	0.958	0.003	0.1596	0.4299	0.74	99.6	99.5	99.6	99.5	99.6	3.6	99.5
2.668-2.737	7.18	0.4922	3.6	66206	66206	9221	9221	0.955	-0.02	0.1957	0.5301	0.742	99.5	99.3	99.5	99.3	99.5	3.63	99.3
2.604-2.668	7.22	0.6	3.02	66565	66565	9222	9222	0.963	0.015	0.2383	0.646	0.738	99.4	99.3	99.4	99.3	99.4	3.65	99.3
2.546-2.604	7.28	0.6709	2.69	67164	67164	9221	9221	0.895	-0.02	0.2641	0.7213	0.722	99.4	99.2	99.4	99.2	99.4	3.68	99.2
2.491-2.546	7.31	0.7851	2.32	67408	67408	9221	9221	0.88	-0.01	0.3081	0.8437	0.718	95.6	95.6	95.6	95.6	95.6	3.69	95.6
2.433-2.491	7.32	0.8774	2.11	67517	67517	9222	9222	0.849	-0.01	0.3439	0.9428	0.731	81.6	81.8	81.6	81.8	81.6	3.7	81.8
2.364-2.433	7.38	0.9322	2.01	68023	68023	9221	9221	0.837	-0.012	0.363	1.0009	0.723	72.9	73.1	72.9	63.6	63.2	3.74	73.1
2.28-2.364	7.55	1.0145	1.94	69657	69657	9222	9222	0.799	-0.029	0.3917	1.0879	0.715	79.3	79.3	79.3	45.2	44.7	3.84	79.3
2.062-2.28	7.03	1.1619	1.52	64815	64815	9221	9221	0.995	-0.029	0.4746	1.2577	0.742	66.5	65.4	66.5	13.2	13.1	3.56	65.4

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Processing

Software

Name	Version	Classification
autoPROC	1.0.5 20230726	data processing
XDS	Jun 30, 2023	data reduction
Aimless	0.7.13	data scaling
STARANISO	2.3.94	data scaling
BUSTER	2.10.4	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.062→188.98 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.919 / SU R Cruickshank DPI: 0.297 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.307 / SU R_free Blow DPI: 0.216 / SU R_free Cruickshank DPI: 0.216

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2348	9442	-	RANDOM
R_work	0.1987	-	-	-
obs	0.2005	184429	68.5 %	-

Displacement parameters

B_iso mean: 41.02 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.7381 Å²	0 Å²	-0.7241 Å²
2-	-	-0.6922 Å²	0 Å²
3-	-	-	-0.0459 Å²

Refine analyze

Luzzati coordinate error obs: 0.28 Å

Refinement step

Cycle: LAST / Resolution: 2.062→188.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25905	0	364	2108	28377

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	27079	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.91	36853	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		9668	SINUSOIDAL	2
X-RAY DIFFRACTION	t_gen_planes		4770	HARMONIC	5
X-RAY DIFFRACTION	t_it		26979	HARMONIC	10
X-RAY DIFFRACTION	t_chiral_improper_torsion		3614	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_ideal_dist_contact		25393	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_omega_torsion	3.01
X-RAY DIFFRACTION	t_other_torsion	16.01

LS refinement shell

Resolution: 2.062→2.21 Å

	R_factor	Num. reflection	% reflection
R_free	0.3311	194	-
R_work	0.2751	-	-
obs	-	-	7.19 %

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