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

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Basic information

Entry
Database: PDB / ID: 9hyh
TitleProtein kinase CK2 catalytic subunit alpha (CSNK2A1 gene product) in complex with F2X-Entry screen fragment D02 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-SY4 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 10, 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)85,6766
Polymers84,4762
Non-polymers1,2004
Water7,314406
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8383
Polymers42,2381
Non-polymers6002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8383
Polymers42,2381
Non-polymers6002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.172, 127.172, 124.930
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 224 or resid 226...
d_2ens_1(chain "B" and (resid 2 through 224 or resid 226...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERSERSERAA2 - 22422 - 244
d_12ILEILEILEILEAA226 - 258246 - 278
d_13LYSLYSGLNGLNAA260 - 310280 - 330
d_14ARGARGALAALAAA312 - 332332 - 352
d_21SERSERSERSERBB2 - 22422 - 244
d_22ILEILEILEILEBB226 - 258246 - 278
d_23LYSLYSGLNGLNBB260 - 310280 - 330
d_24ARGARGALAALABB312 - 332332 - 352

NCS oper: (Code: givenMatrix: (0.00693977011846, -0.99997377791, 0.00206956091602), (0.997136592916, 0.00676420009592, -0.0753183952596), (0.0753024213297, 0.00258632726942, 0.997157387905)Vector: - ...NCS oper: (Code: given
Matrix: (0.00693977011846, -0.99997377791, 0.00206956091602), (0.997136592916, 0.00676420009592, -0.0753183952596), (0.0753024213297, 0.00258632726942, 0.997157387905)
Vector: -61.9469201019, 62.7643435865, 32.8300466193)

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Components

#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
#2: Chemical ChemComp-SY4 / ~{N}-[5-azanyl-2,4-bis(fluoranyl)phenyl]propane-1-sulfonamide


Mass: 250.266 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12F2N2O2S / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 200 mM Li2SO4, 100 mM Bis-Tris/HCl, pH 6.5, 35 % 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 % 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 plus 2 microliter reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.96→72.984 Å / Num. obs: 73855 / % possible obs: 100 % / Redundancy: 26.3 % / Biso Wilson estimate: 31.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.34 / Rpim(I) all: 0.067 / Net I/σ(I): 8.9
Reflection shellResolution: 1.96→1.993 Å / Rmerge(I) obs: 4.378 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3609 / CC1/2: 0.349 / Rpim(I) all: 0.887

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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: 1.96→72.98 Å / SU ML: 0.235 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7648
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.241 1098 1.49 %
Rwork0.2005 72370 -
obs0.2011 73468 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.99 Å2
Refinement stepCycle: LAST / Resolution: 1.96→72.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5597 0 82 406 6085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00635876
X-RAY DIFFRACTIONf_angle_d0.80167961
X-RAY DIFFRACTIONf_chiral_restr0.0525812
X-RAY DIFFRACTIONf_plane_restr0.0081022
X-RAY DIFFRACTIONf_dihedral_angle_d13.70652205
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.557401622955 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.050.31361350.32258884X-RAY DIFFRACTION99.23
2.05-2.160.29961340.27048908X-RAY DIFFRACTION99.37
2.16-2.290.2421360.23688954X-RAY DIFFRACTION99.78
2.29-2.470.2491370.21098944X-RAY DIFFRACTION99.31
2.47-2.720.2711400.20419000X-RAY DIFFRACTION99.36
2.72-3.110.21691350.18999042X-RAY DIFFRACTION99.45
3.11-3.920.23791360.18259133X-RAY DIFFRACTION99.52
3.92-72.980.22281450.1799505X-RAY DIFFRACTION99.79
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)
10.1804597345740.1126184491440.4393710152480.2428641274170.05029161167741.46882567936-0.08527129042-0.2215902415430.04317254491690.2619251415830.0826339571421-0.0217800213041-0.3024148467290.04152652618660.002025042916480.3188334281340.01808320863090.02992981262060.3332061499280.02634200494310.27751274192-46.6435670675-1.60080263645-8.03317669437
20.473828032406-0.40800520764-0.006401948744450.451447416816-0.224125705590.414919940159-0.117006950568-0.08475462830730.178878926285-0.0682835802688-0.1057742618370.0178107108048-0.01082167473490.0137671021083-2.40392153498E-50.41863458896-0.037514212245-0.02084474474960.2588897033110.01133814182220.325131953283-51.564427073910.1263532592-22.5145919975
30.220480826094-0.1342704476910.2336977398980.3993930399640.1833610868190.578944104145-0.02026034841790.06086421422480.1100383094690.134237537607-0.1178672256730.000731689440972-0.228583784534-0.174428216701-2.61607808762E-50.2661093882340.05045521580690.02215656181760.3579692644850.001589311264610.32574741991-49.28639898035.23110094986-12.8173930649
40.866834851814-0.0501032137996-0.2277219882830.9664969680050.4817389130240.2525589791890.04573348878560.4265064123860.180853734695-0.432489127839-0.00913112652265-0.229946951917-0.204780456610.22539264153-0.0007312711297780.3376210663810.03335435873570.02164005908230.4322230590430.06249513106260.372690876394-35.1217195058-0.699247633839-26.7660788807
50.815986122077-0.442470087480.1989285526271.062545912160.5690250593270.5933349792590.04957115339340.0619660702524-0.0334029082965-0.07044367371680.005987321245050.11922879230.03051563323590.069255429956-2.27832825535E-50.1951834314440.0685996782972-0.01819066283420.2540864278030.01929661262330.2532007899-42.6800698835-9.89116951775-20.8708338277
61.03812769313-0.3103888475380.08896332715540.4139364205920.2285987693680.8483342200790.147094817050.376191876987-0.262292116656-0.274964050652-0.0437189477450.3632883163620.330471571291-0.353053810790.0001543766262360.3922040444760.020055767613-0.07594758030120.38113765435-0.04006145289160.412947191787-46.2016702334-26.9649430392-28.2948874896
71.11726498788-0.42144414029-0.07911108458560.6757851330010.06792888402370.5885232466920.01697887551680.2252439653540.0423055072287-0.192991419951-0.00297647385394-0.1544278276440.2307727244570.3983291782310.0001770737071710.3191790106470.1348305407280.01218769985480.458702890553-0.01362060890730.307660583995-28.2297884392-15.5640623239-27.6815781951
80.9820100787350.37722752583-0.31213136110.600804645419-0.02523728133820.7450550802920.224343137501-0.1788427233740.02112084528240.272838012989-0.1777979606810.02013888022560.00699258937923-0.07808373867953.74287761181E-50.308201850063-0.0262670250119-0.004958106260110.3175359258020.002229931070870.249100298696-60.652542745816.843429829721.2719165671
90.5819687408270.4039372367720.4864432015040.5062217151730.1482194072450.5404433657150.129120565350.3024741443890.427308020528-0.0413352830045-0.244796078698-0.389381627096-0.06423382453790.149801682064-0.001781221168220.2671903851450.00907934501480.005982290286010.417079649879-0.01840854215810.292805807085-72.77443956313.06173859266.4413271359
100.550255134924-0.0904716929675-0.03661122155710.008983523651470.00453461207302-0.000101441118580.0558359674032-0.08452725631780.116184703056-0.0203413672775-0.1742070117060.1096490606750.0324322891523-0.100732308296-3.50868412242E-50.255065350863-0.02389557974090.01791699046880.2475609790090.03212075667620.31321387509-67.626842379414.62772029116.4280047035
110.1696820778920.313776407964-0.1425262123660.620974601241-0.2749675570030.107499798865-0.192764960010.6305177195190.186648833677-0.2424448056950.3043010643630.195464792350.0441396320732-0.09978339306540.112227643450.30578267341-0.155224952455-0.04509819980980.4657499537090.1175467910370.312318603065-61.672038693229.83440788173.4559755988
121.3378924690.694759431953-0.06617699606441.146110239980.2548181498260.512723790188-0.1200585809820.358043749713-0.0578250455653-0.145042296660.195147378591-0.03019937594090.0671316603431-0.01648367892520.03722295019910.22660142597-0.1046719569150.006591101821490.3438735872480.000355006390340.225693276266-50.07330575820.98251972946.05645468861
131.412684328020.8970695405170.2870469872261.848606541730.3791161541471.31944734075-0.1304146952190.4243551219230.0562787438145-0.2171463247670.308869650728-0.216218240618-0.09397306164810.2913470140270.324966419880.27850934424-0.1718647757460.03680587893470.492404125549-0.008002560616380.290206449804-40.224818793329.47965412523.61788521094
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 227 )AA150 - 227149 - 226
66chain 'A' and (resid 228 through 280 )AA228 - 280227 - 279
77chain 'A' and (resid 281 through 333 )AA281 - 333280 - 332
88chain 'B' and (resid 2 through 44 )BD2 - 441 - 43
99chain 'B' and (resid 45 through 74 )BD45 - 7444 - 73
1010chain 'B' and (resid 75 through 108 )BD75 - 10874 - 107
1111chain 'B' and (resid 109 through 149 )BD109 - 149108 - 148
1212chain 'B' and (resid 150 through 249 )BD150 - 249149 - 248
1313chain 'B' and (resid 250 through 332 )BD250 - 332249 - 331

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