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

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Basic information

Entry
Database: PDB / ID: 9qag
TitleProtein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment F08 and CX-4945 (Silmitasertib)
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
Chem-3NG / 4-[(methylamino)methyl]phenol / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 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)43,9554
Polymers43,4331
Non-polymers5223
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area15110 Å2
Unit cell
Length a, b, c (Å)46.539, 47.813, 50.407
Angle α, β, γ (deg.)113.297, 90.041, 91.219
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-RBJ / 4-[(methylamino)methyl]phenol


Mass: 137.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 381 / 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: 48.13 %
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: 1.007→46.526 Å / Num. obs: 175900 / % possible obs: 49.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 9.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.034 / Net I/σ(I): 5.7
Reflection shellResolution: 1.007→1.156 Å / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5226 / CC1/2: 0.507 / Rpim(I) all: 0.486

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PHASER1.20.1_4487phasing
XDSdata reduction
Aimlessdata scaling
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.01→32.98 Å / SU ML: 0.0713 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.2299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1617 1045 0.99 %
Rwork0.1355 104441 -
obs0.1357 105486 50 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.41 Å2
Refinement stepCycle: LAST / Resolution: 1.01→32.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 36 381 3176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212890
X-RAY DIFFRACTIONf_angle_d1.17153904
X-RAY DIFFRACTIONf_chiral_restr0.0966399
X-RAY DIFFRACTIONf_plane_restr0.013499
X-RAY DIFFRACTIONf_dihedral_angle_d13.32831092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.060.388810.2094183X-RAY DIFFRACTION0.61
1.06-1.130.3027210.18142255X-RAY DIFFRACTION7.58
1.13-1.210.2091950.17949969X-RAY DIFFRACTION33.45
1.21-1.340.20711800.168717528X-RAY DIFFRACTION58.65
1.34-1.530.17732220.149923079X-RAY DIFFRACTION77.23
1.53-1.930.15642630.132425918X-RAY DIFFRACTION86.93
1.93-32.980.14922630.125325509X-RAY DIFFRACTION85.52

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