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- PDB-9qak: Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product... -

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Basic information

Entry
Database: PDB / ID: 9qak
TitleProtein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment G07
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / CK2 / fragment-based screening / protein kinase / protein kinase CK2 / casein kinase II
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / : / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / : / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / liver regeneration / acrosomal vesicle / Signal transduction by L1 / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / chromatin / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsWerner, C. / Harasimowicz, H. / Barthel, T. / Weiss, M.S. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
CitationJournal: Kinases Phosphatases / Year: 2026
Title: Crystallographic Fragment Screening with CK2 alpha', an Isoform of Human Protein Kinase CK2 Catalytic Subunit, and Its Use to Obtain a CK2 alpha'/Heparin Complex Structure
Authors: Werner, C. / Barthel, T. / Harasimowicz, H. / Marminon, C. / Weiss, M.S. / Borgne, M.L. / Niefind, K.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6413
Polymers43,4331
Non-polymers2092
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area15250 Å2
Unit cell
Length a, b, c (Å)46.537, 47.758, 50.575
Angle α, β, γ (deg.)66.677, 89.800, 88.776
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Casein kinase II subunit alpha' / CK II alpha'


Mass: 43432.535 Da / Num. of mol.: 1 / Mutation: C336S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P19784, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1I5I / 2-[(4-methyl-1,2,4-triazol-3-yl)sulfanyl]ethanoic acid


Mass: 173.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 ...Details: Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.98→46.53 Å / Num. obs: 219026 / % possible obs: 51.7 % / Redundancy: 7 % / Biso Wilson estimate: 9.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.031 / Net I/σ(I): 13.3
Reflection shellResolution: 0.98→1.147 Å / Rmerge(I) obs: 1.041 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5891 / CC1/2: 0.639 / Rpim(I) all: 0.42

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.98→46.53 Å / SU ML: 0.085 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.017
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1752 1192 1.01 %
Rwork0.1473 117382 -
obs0.1476 118574 51.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.67 Å2
Refinement stepCycle: LAST / Resolution: 0.98→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 12 289 3060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01352873
X-RAY DIFFRACTIONf_angle_d1.25453881
X-RAY DIFFRACTIONf_chiral_restr0.1006400
X-RAY DIFFRACTIONf_plane_restr0.0145500
X-RAY DIFFRACTIONf_dihedral_angle_d13.55141094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-1.020.708210.201375X-RAY DIFFRACTION0.3
1.02-1.070.2119100.245608X-RAY DIFFRACTION2.44
1.07-1.120.2246330.2093217X-RAY DIFFRACTION12.79
1.12-1.190.251610.18966935X-RAY DIFFRACTION27.65
1.19-1.290.1831270.190612394X-RAY DIFFRACTION49.4
1.29-1.420.21512190.185520365X-RAY DIFFRACTION81.26
1.42-1.620.19712480.166724359X-RAY DIFFRACTION97.16
1.62-2.040.16552460.147924574X-RAY DIFFRACTION98.02
2.04-46.530.16252470.129924855X-RAY DIFFRACTION98.98

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