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- PDB-9hic: K166 acetylated human muscle pyruvate kinase, isoform M2 (PKM2), ... -

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Basic information

Entry
Database: PDB / ID: 9hic
TitleK166 acetylated human muscle pyruvate kinase, isoform M2 (PKM2), in complex with FBP
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / acetylation / post-translational modification / glycolysis / genetic code expansion / acetylated lysine / metabolism
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding ...pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / Regulation of pyruvate metabolism / glycolytic process / non-specific protein-tyrosine kinase / cellular response to insulin stimulus / MHC class II protein complex binding / extracellular vesicle / : / protein tyrosine kinase activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cilium / cadherin binding / intracellular membrane-bounded organelle / mRNA binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytoplasm / 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 / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPavlenko, D. / Nudelman, H. / Shahar, A. / Arbely, E.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
European Research Council (ERC)678461European Union
Israel Science Foundation1769/20 Israel
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Isoform-specific regulation of PKM by acetylation
Authors: Pavlenko, D. / Tamargo-Azpilicueta, J. / Ankri, Y. / Nudelman, H. / Shahar, A. / Diez-Moreno, I. / Arbely, E.
History
DepositionNov 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase PKM
B: Pyruvate kinase PKM
C: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,02913
Polymers235,5474
Non-polymers1,4829
Water84747
1
A: Pyruvate kinase PKM
B: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules

C: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,02913
Polymers235,5474
Non-polymers1,4829
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
2
C: Pyruvate kinase PKM
hetero molecules

A: Pyruvate kinase PKM
B: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,02913
Polymers235,5474
Non-polymers1,4829
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)75.998, 147.230, 97.969
Angle α, β, γ (deg.)90.00, 103.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyruvate kinase PKM / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate kinase 2/3 / Pyruvate kinase muscle isozyme / Threonine-protein kinase PKM2 / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / Tyrosine-protein kinase PKM2 / p58


Mass: 58886.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P14618, pyruvate kinase, non-specific serine/threonine protein kinase, non-specific protein-tyrosine 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.: 4 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2 0.1M Bis-Tris pH 5.5 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.9→49.38 Å / Num. obs: 46401 / % possible obs: 99.81 % / Redundancy: 7.1 % / CC1/2: 0.992 / Net I/σ(I): 8.03
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 4616 / CC1/2: 0.592

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.38 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 53.56 / SU ML: 0.427 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25205 2326 5 %RANDOM
Rwork0.19693 ---
obs0.19965 44050 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.737 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å2-0.31 Å2
2--0.86 Å20 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 2.9→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15906 0 85 47 16038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01216303
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2491.82622049
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85252082
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.5855132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.051102922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1410.22542
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211985
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1311.8358319
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5993.29110398
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3061.9987984
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.31620.4523967
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 186 -
Rwork0.334 3219 -
obs--99.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.912-0.11340.22612.51010.5991.74290.02050.08870.0485-0.152-0.10140.31330.0062-0.09320.0810.5867-0.0569-0.17540.3076-0.00670.0844-3.4022-9.0995-1.2117
21.5583-0.14230.14742.34460.08171.3975-0.05230.06460.3731-0.08010.0213-0.2173-0.15930.0950.0310.5052-0.037-0.21910.3402-0.04770.23433.531418.530818.8671
31.8489-0.01720.59620.97190.20412.5981-0.0015-0.0841-0.2404-0.00850.1214-0.15190.19710.4093-0.11990.60370.1538-0.15380.5025-0.03790.0996-37.2524-30.037631.9089
41.7492-0.6453-0.02741.70320.39791.624-0.2172-0.5486-0.31560.27610.29130.18470.2318-0.2015-0.07410.62010.1582-0.13410.8160.10340.120213.6934-24.655855.8094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 611
2X-RAY DIFFRACTION2B14 - 611
3X-RAY DIFFRACTION3C14 - 611
4X-RAY DIFFRACTION4D14 - 611

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