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- PDB-9q9d: Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product... -

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Basic information

Entry
Database: PDB / ID: 9q9d
TitleProtein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment D06 and CX-4945 (Silmitasertib)
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / fragment-based screening / 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
Chem-3NG / (3-methoxyphenyl)(pyrrolidin-1-yl)methanone / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 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 26, 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)44,0585
Polymers43,4331
Non-polymers6264
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-17 kcal/mol
Surface area14990 Å2
Unit cell
Length a, b, c (Å)46.513, 47.804, 50.522
Angle α, β, γ (deg.)113.442, 90.113, 91.246
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-3NG / 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 349.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12ClN3O2
#3: Chemical ChemComp-R9G / (3-methoxyphenyl)(pyrrolidin-1-yl)methanone


Mass: 205.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
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: 0.89→46.35 Å / Num. obs: 183402 / % possible obs: 60.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 8.88 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 1.206 / Rpim(I) all: 0.616 / Net I/σ(I): 10.1
Reflection shellResolution: 0.89→1.026 Å / Rmerge(I) obs: 1.224 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 9170 / CC1/2: 0.345 / Rpim(I) all: 0.656

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.89→32.64 Å / SU ML: 0.0735 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.1985
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1585 1829 1.01 %
Rwork0.148 179799 -
obs0.1482 181628 59.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.45 Å2
Refinement stepCycle: LAST / Resolution: 0.89→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 42 275 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01342886
X-RAY DIFFRACTIONf_angle_d1.23813901
X-RAY DIFFRACTIONf_chiral_restr0.1014399
X-RAY DIFFRACTIONf_plane_restr0.0157498
X-RAY DIFFRACTIONf_dihedral_angle_d13.87211090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.89-0.920.008410.4681108X-RAY DIFFRACTION0.46
0.92-0.940.408780.3696567X-RAY DIFFRACTION2.48
0.94-0.970.3851130.33191182X-RAY DIFFRACTION5.14
0.97-1.010.2952330.31163212X-RAY DIFFRACTION13.88
1.01-1.050.2561930.28527480X-RAY DIFFRACTION32.42
1.05-1.10.20461440.252613528X-RAY DIFFRACTION58.36
1.1-1.150.22121840.209719070X-RAY DIFFRACTION82.51
1.15-1.230.21812090.185521486X-RAY DIFFRACTION92.37
1.23-1.320.17912320.159722111X-RAY DIFFRACTION95.65
1.32-1.450.16642260.137222482X-RAY DIFFRACTION97.2
1.45-1.660.12872300.122922643X-RAY DIFFRACTION97.93
1.66-2.10.13392340.125322873X-RAY DIFFRACTION98.69
2.1-32.640.14262220.132823057X-RAY DIFFRACTION99.56

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