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- PDB-14cv: Structure of liver pyruvate kinase in complex with allosteric sit... -

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Basic information

Entry
Database: PDB / ID: 14cv
TitleStructure of liver pyruvate kinase in complex with allosteric site binder 8h
ComponentsIsoform L-type of Pyruvate kinase PKLR
KeywordsTRANSFERASE / Pyruvate kinase / fluorescence / allosteric site
Function / homology
Function and homology information


pyruvate kinase complex / SARS-CoV-1-host interactions / pyruvate biosynthetic process / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion ...pyruvate kinase complex / SARS-CoV-1-host interactions / pyruvate biosynthetic process / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion / canonical glycolysis / response to ATP / Regulation of gene expression in beta cells / potassium ion binding / response to glucose / response to cAMP / cellular response to epinephrine stimulus / response to nutrient / glycolytic process / cellular response to insulin stimulus / response to hypoxia / magnesium ion binding / extracellular exosome / cytosol
Similarity search - Function
Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / : / OXALATE ION / : / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.074 Å
AuthorsLulla, A. / Rodriguez Rivero, A. / Grotli, M. / Hyvonen, M.
CitationJournal: Rsc Med Chem / Year: 2026
Title: Symmetry-Guided Fusion Converts Weak Liver Pyruvate Kinase inhibitors into potent Allosteric Activators
Authors: Monjas, L. / Rodriguez-Rivero, A. / Fuchtbauer, A.F.F. / Nilsson, O. / Haversen, L. / Lulla, A. / Brear, P. / Rutberg, M. / Bergh, P.O. / Boren, J. / MARDINOGLU, A. / Hyvonen, M. / Grotli, M.
History
DepositionApr 28, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)392,27245
Polymers386,2838
Non-polymers5,98937
Water5,206289
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


Theoretical massNumber of molelcules
Total (without water)196,15623
Polymers193,1424
Non-polymers3,01419
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21930 Å2
ΔGint-105 kcal/mol
Surface area54870 Å2
MethodPISA
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


Theoretical massNumber of molelcules
Total (without water)196,11722
Polymers193,1424
Non-polymers2,97518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22240 Å2
ΔGint-125 kcal/mol
Surface area53810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.654, 112.558, 184.1
Angle α, β, γ (deg.)90, 94.19, 90
Int Tables number5
Space group name H-MC121

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Components

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


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
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 318 molecules

#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-WWI / 2,6-bis(3,5-dihydroxybenzene-1-sulfonyl)naphthalene-1,5-diol


Mass: 504.486 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H16O10S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.00002
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 3.074→98.337 Å / Num. obs: 48012 / % possible obs: 91.5 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.064 / Net I/σ(I): 6 / Num. measured all: 339339
Reflection shellResolution: 3.074→3.385 Å / % possible obs: 79.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 1.154 / Num. measured all: 17633 / Num. unique obs: 2402 / CC1/2: 0.815 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.4refinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.074→101.06 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.831
RfactorNum. reflection% reflectionSelection details
Rfree0.3199 2369 -RANDOM
Rwork0.3063 45644 --
obs0.307 48013 62.3 %-
Displacement parametersBiso mean: 82.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.3319 Å20 Å2-5.2935 Å2
2---0.0388 Å20 Å2
3---2.3707 Å2
Refine analyzeLuzzati coordinate error obs: 0.675 Å
Refinement stepCycle: LAST / Resolution: 3.074→101.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25832 0 361 289 26482
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00727196HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8536997HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9754SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4940HARMONIC5
X-RAY DIFFRACTIONt_it27138HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3649SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact23425SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.16
X-RAY DIFFRACTIONt_other_torsion19.34
LS refinement shellResolution: 3.07→3.24 Å
RfactorNum. reflection% reflection
Rfree0.4821 46 -
Rwork0.3654 915 -
obs0.371 961 8.51 %

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