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- PDB-9hzh: Protein kinase CK2 catalytic subunit alpha (CSNK2A1 gene product)... -

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Basic information

Entry
Database: PDB / ID: 9hzh
TitleProtein kinase CK2 catalytic subunit alpha (CSNK2A1 gene product) in complex with F2X-Entry screen fragment F02 and CX-4945 (Silmitasertib)
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein kinase CK2 / kinase / fragment-based screening / ligand / casein kinase II
Function / homology
Function and homology information


positive regulation of aggrephagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / negative regulation of signal transduction by p53 class mediator ...positive regulation of aggrephagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / negative regulation of signal transduction by p53 class mediator / 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 / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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 / Chem-T9Y / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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
DepositionJan 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,29314
Polymers84,4762
Non-polymers1,81612
Water6,720373
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1467
Polymers42,2381
Non-polymers9086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1467
Polymers42,2381
Non-polymers9086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.488, 129.488, 123.731
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 42238.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 385 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-3NG / 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 349.770 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H12ClN3O2
#4: Chemical ChemComp-T9Y / ethyl 5-(trifluoromethyl)-1H-pyrazole-4-carboxylate


Mass: 208.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7F3N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir:200 mM Li2SO4, 100 mM Bis-Tris/HCl, pH 6.5, 35 % (w/v) PEG 3350 Protein/Ligand mix: 5 mg per mL CK2alpha1-335, 100 mM ligand/0.5 mM CX-4945, 10 % DMSO prequilibrated Drop: 4 ...Details: Reservoir:200 mM Li2SO4, 100 mM Bis-Tris/HCl, pH 6.5, 35 % (w/v) PEG 3350 Protein/Ligand mix: 5 mg per mL CK2alpha1-335, 100 mM ligand/0.5 mM CX-4945, 10 % DMSO prequilibrated Drop: 4 microliter protein/ligand mix, 2 microliter reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.07→91.562 Å / Num. obs: 46064 / % possible obs: 71.5 % / Redundancy: 26.1 % / Biso Wilson estimate: 28.07 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.065 / Net I/σ(I): 11.9
Reflection shellResolution: 2.07→2.304 Å / Rmerge(I) obs: 2.358 / Mean I/σ(I) obs: 1 / Num. unique obs: 2303 / CC1/2: 0.168 / Rpim(I) all: 0.551

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Processing

Software
NameVersionClassification
PHENIX2.0_5885refinement
XDSdata reduction
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→91.56 Å / SU ML: 0.3172 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.2891
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2557 1160 2.52 %
Rwork0.2146 44858 -
obs0.2157 46018 71.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.94 Å2
Refinement stepCycle: LAST / Resolution: 2.07→91.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5586 0 116 373 6075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00175857
X-RAY DIFFRACTIONf_angle_d0.43347929
X-RAY DIFFRACTIONf_chiral_restr0.0412807
X-RAY DIFFRACTIONf_plane_restr0.00431012
X-RAY DIFFRACTIONf_dihedral_angle_d10.80382185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.170.2611130.3716478X-RAY DIFFRACTION6.2
2.17-2.280.3602350.34091359X-RAY DIFFRACTION17.69
2.28-2.420.35671270.2984706X-RAY DIFFRACTION60.76
2.42-2.610.35311920.28467702X-RAY DIFFRACTION99.25
2.61-2.870.3031870.2587319X-RAY DIFFRACTION93.98
2.87-3.290.28272060.2167816X-RAY DIFFRACTION100
3.29-4.140.21361900.17977281X-RAY DIFFRACTION92.04
4.14-91.560.2042100.17868197X-RAY DIFFRACTION99.66
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)
11.41405378167370.37167633227550.468082309522790.219807345118270.185726610098840.74440234072757-0.034273931945967-0.31702214645117-0.29840529666190.602124225157320.0820322654822880.05448651483215-0.256369438817510.077039200804553-0.00595534201863390.374948546642660.00255917469632290.0740204374483620.241822938158880.0141502509472120.093811806205266-47.853233827186-2.6209222999489-8.2416323226531
22.7850394877999-1.28451858704310.260793303415191.94721305682990.110600230227743.607600303593-0.542314697510460.331258853487820.66105764417867-0.26540748917471-0.53548953675614-0.45145702754327-0.27239924744275-0.016521925133479-2.89200350922630.31143065102210.032108547069036-0.00694763300855790.110674299030880.0544760479456930.082408161695603-52.055037251539.3753814793573-22.6717180975
31.8970431694752-1.46342872461111.07834815750471.1889355353964-0.653498634917580.92525105531197-0.416696539676770.00196722416374520.464505853741840.37219497146217-0.092469472179259-0.30001145107052-0.25052380723449-0.089563076494005-0.845461846883670.16198083456046-0.00913090554590630.0449305723231790.21749693208725-0.0393913981327960.18959518579203-50.2304433474264.2775821174685-13.07284149573
41.2953277050069-0.644445683940280.336081336448131.00768601867880.832642730128821.38177318649910.126758353790440.638554031567980.22878746037081-0.25637968183377-0.051645664169237-0.34558169821777-0.791282548659390.48134288798840.00818067542097550.187682475963680.170373411834820.0122232263495270.247807439892830.0833466028674350.25965640674544-35.710486266405-1.8124436608168-26.619822592113
51.6740660164316-0.24829159299842-0.421052864555481.4583877933190.228232121573411.24357234389320.156255801964280.28606741517302-0.14828478453061-0.13078029540341-0.147084260846220.00163119421948790.023161956883141-0.00273553257453280.063449741351460.117208532563410.059909467147561-0.0601813076026960.2160815311387-0.00554404134605580.18557276786849-44.537030273476-13.164306953309-23.695811988333
60.6351437863636-0.203274502225930.496164697416720.60861009685716-0.751653449879121.09713302669290.360154838314040.36264721970671-0.85891690121947-0.51071928710538-0.0398169039047090.775330606432950.43575336207384-0.449353661180710.299933445299080.340425230585780.051605296022462-0.154726716053630.41443106252554-0.10872852642610.75688880084769-47.127748318631-33.079614819198-25.876285528582
70.86766620282373-0.222833703974260.0109914692017771.13364600164910.00914659869803230.630306442906780.250539342486160.41070681107095-0.1532129570746-0.2128413526127-0.039006200605779-0.36468788883770.00937884501943250.278649161508490.552918805376340.270388271450120.15891366528474-0.0138308582037060.407432987975520.00719435431647910.27746843708254-29.972841367948-18.092880575345-27.729799337056
80.00011611975493183-0.00039444417635752-0.0024720544301705-0.00023576504192790.0012321921418918-0.0036402284508671-0.0078511594870694-0.056351790740810.0750370936170380.063470118555289-0.00527029914714710.0064547239985609-0.00222548558841390.19570444278365-0.162599515678770.59544198714842-0.78851743431001-0.397090720362510.44637761924034-0.166254460838261.3886204777283-18.982382412119-2.1349574504357-22.675849627921
90.21258401837239-0.0479626141122460.014555350833311.51941358374030.453950334929211.89479743798620.18633256818210.0036955561375648-0.165481722121920.48393513616967-0.15236179762193-0.103087771874770.043043149251-0.26838695103144-0.0108503252484240.063680209989621-0.0120254733394640.0905285861237370.20248887551344-0.0397805008109840.01141303328583-65.65337257406215.19658009516915.437809002978
101.57777762334321.1913876585817-0.665572250930351.90715279500520.686073932634231.7203531309107-0.246256901100990.323768076757470.042386076655022-0.132334641965570.21454232746018-0.017607506287553-0.094809134925813-0.11402738797181-0.0688687060454570.14172943487863-0.071854400289154-0.0324012154510920.160658432681760.0395601385408980.034393024633492-56.00874907554622.6861106634275.7130521918344
111.51143357437240.781657129311130.445535486901311.76134995061590.0410152545371591.4337411826107-0.20822101716650.357086848457510.096122422206722-0.111046819617410.29000742096511-0.38626619968558-0.0446621084328790.42949007474480.169881301472540.24230153851839-0.155828605198450.00563197337662750.39330353559696-0.0247375920000350.26059982672508-40.73126340408129.6783557217132.7773412958371
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 44 )AA2 - 441 - 43
22chain 'A' and (resid 45 through 74 )AA45 - 7444 - 73
33chain 'A' and (resid 75 through 108 )AA75 - 10874 - 107
44chain 'A' and (resid 109 through 149 )AA109 - 149108 - 148
55chain 'A' and (resid 150 through 249 )AA150 - 249149 - 248
66chain 'A' and (resid 250 through 280 )AA250 - 280249 - 279
77chain 'A' and (resid 281 through 329 )AA281 - 329280 - 328
88chain 'A' and (resid 330 through 332 )AA330 - 332329 - 331
99chain 'B' and (resid 2 through 87 )BH2 - 871 - 86
1010chain 'B' and (resid 88 through 249 )BH88 - 24987 - 248
1111chain 'B' and (resid 250 through 332 )BH250 - 332249 - 331

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