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- PDB-9fbl: Structure of human protein kinase CK2 catalytic subunit (CK2alpha... -

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Basic information

Entry
Database: PDB / ID: 9fbl
TitleStructure of human protein kinase CK2 catalytic subunit (CK2alpha, CSNK2A1 gene product) in complex with the cyclic peptidomimetic compound 15 discovered by high-throughput screening
Components
  • Casein kinase II subunit alpha
  • Cyclic peptidomimetic compound FMP35
KeywordsTRANSFERASE / HUMAN PROTEIN KINASE CK2 CATALYTIC SUBUNIT ALPHA / CSNK2A1 GENE PRODUCT / INHIBITION OF CK2ALPHA/CK2BETA SUBUNIT INTERACTION
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / 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 / Regulation of PTEN stability and activity / Wnt signaling pathway / 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
NICOTINIC ACID / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsWerner, C. / Niefind, K. / Eimermacher, S. / Pietsch, M. / Lindenblatt, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
Citation
Journal: To Be Published
Title: Structure of human protein kinase CK2 catalytic subunit (CK2alpha, CSNK2A1 gene product) in complex with the cyclic peptidomimetic compound 15 discovered by high-throughput screening
Authors: Werner, C. / Niefind, K. / Eimermacher, S. / Pietsch, M. / Lindenblatt, D.
#1: Journal: Anal Biochem / Year: 2015
Title: Development of a high-throughput screening-compatible assay to identify inhibitors of the CK2alpha/CK2beta interaction.
Authors: Hochscherf, J. / Lindenblatt, D. / Steinkrueger, M. / Yoo, E. / Ulucan, O. / Herzig, S. / Issinger, O.G. / Helms, V. / Goetz, C. / Neundorf, I. / Niefind, K. / Pietsch, M.
#2: Journal: ACS Chem Biol / Year: 2013
Title: First structure of protein kinase CK2 catalytic subunit with an effective CK2beta-competitive ligand.
Authors: Raaf, J. / Guerra, B. / Neundorf, I. / Bopp, B. / Issinger, O.G. / Jose, J. / Pietsch, M. / Niefind, K.
History
DepositionMay 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
B: Casein kinase II subunit alpha
C: Casein kinase II subunit alpha
L: Cyclic peptidomimetic compound FMP35
N: Cyclic peptidomimetic compound FMP35
P: Cyclic peptidomimetic compound FMP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,89923
Polymers127,2586
Non-polymers1,64117
Water3,495194
1
A: Casein kinase II subunit alpha
L: Cyclic peptidomimetic compound FMP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1199
Polymers42,4192
Non-polymers6997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
N: Cyclic peptidomimetic compound FMP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8316
Polymers42,4192
Non-polymers4114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase II subunit alpha
P: Cyclic peptidomimetic compound FMP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9508
Polymers42,4192
Non-polymers5306
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.952, 206.560, 76.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-513-

HOH

21B-581-

HOH

31B-582-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 159 or resid 161 through 227 or resid 229 through 331))
d_2ens_1(chain "B" and (resid 3 through 159 or resid 161 through 227 or resid 229 through 331))
d_3ens_1(chain "C" and (resid 3 through 159 or resid 161 through 227 or resid 229 through 331))
d_1ens_2chain "L"
d_2ens_2chain "N"
d_3ens_2chain "P"
d_1ens_3chain "M"
d_2ens_3chain "O"
d_3ens_3chain "Q"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYPROPROAA3 - 15917 - 173
d_12ens_1ASNASNPHEPHEAA161 - 227175 - 241
d_13ens_1LYSLYSGLNGLNAA229 - 331243 - 345
d_21ens_1GLYGLYPROPROBB3 - 15917 - 173
d_22ens_1ASNASNPHEPHEBB161 - 227175 - 241
d_23ens_1LYSLYSGLNGLNBB229 - 331243 - 345
d_31ens_1GLYGLYPROPROCC3 - 15917 - 173
d_32ens_1ASNASNPHEPHECC161 - 227175 - 241
d_33ens_1LYSLYSGLNGLNCC229 - 331243 - 345
d_11ens_2A1ICCA1ICCVALVALLD1 - 51 - 5
d_21ens_2A1ICCA1ICCVALVALNE1 - 51 - 5
d_31ens_2A1ICCA1ICCVALVALPF1 - 51 - 5
d_11ens_3NIONIONIONIOAG401
d_21ens_3NIONIONIONIOBN401
d_31ens_3NIONIONIONIOCR401

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.999994957629, 0.00166421252426, -0.00270464648522), (0.00142848388343, 0.9963854298, 0.0849354738346), (0.00283622102995, 0.0849311820145, -0.996382782956)39.3452149422, -35.7043722711, 7.90771726888
2given(-0.999345327888, 0.0230930402251, -0.0278500829688), (0.025535550143, 0.995541849782, -0.0907984637055), (0.0256291105406, -0.0914501876736, -0.995479789783)36.7647797181, 33.8110367774, 5.82845565329
3given(-0.997448777249, -0.0441496222113, 0.056095878847), (-0.0316719657316, 0.977932414836, 0.206506848796), (-0.0639751776216, 0.204203337073, -0.976835796732)36.8172366622, -39.3644597843, 8.30731244756
4given(-0.993912838111, 0.0952207370921, -0.0554101206089), (0.102409790127, 0.983961671252, -0.146053635327), (0.0406141000678, -0.150839122027, -0.987723672968)36.6916425895, 33.3841013371, 5.88496885284
5given(-0.981784061772, -0.149891297462, 0.116758961097), (-0.152121686456, 0.988307261181, -0.0103802700207), (-0.113837816919, -0.0279527537342, -0.993106034116)37.0711859947, -27.9030052714, 13.2168947369
6given(-0.954960434858, 0.273923797068, -0.114089093498), (0.287887473976, 0.948453244742, -0.132503754159), (0.0719122394527, -0.159380663627, -0.984594553041)34.348980578, 28.6498700815, 5.0718464971

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCLNP

#1: Protein Casein kinase II subunit alpha


Mass: 41685.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Protein/peptide Cyclic peptidomimetic compound FMP35


Mass: 733.876 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 211 molecules

#3: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H5NO2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein solution: 97.5 mikroliter CK2alpha-1-335 solution (7 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter 20 millimolar FMP35 in DMSO and incubated for ...Details: protein solution: 97.5 mikroliter CK2alpha-1-335 solution (7 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter 20 millimolar FMP35 in DMSO and incubated for 30 min. reservoir: 1.5 mol/l lithium sulphate, 100 mM sodium HEPES buffer pH 7.5. crystallization drop: 200 nanoliter protein solution plus 100 nanoliter reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.176→72.931 Å / Num. obs: 39662 / % possible obs: 60.2 % / Redundancy: 17.6 % / Biso Wilson estimate: 38.94 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.479 / Rpim(I) all: 0.116 / Rrim(I) all: 0.493 / Rsym value: 0.479 / Net I/σ(I): 8.1
Reflection shellResolution: 2.176→2.403 Å / Redundancy: 17.7 % / Rmerge(I) obs: 8.397 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1983 / CC1/2: 0.502 / Rpim(I) all: 1.999 / Rrim(I) all: 8.637 / Rsym value: 8.397 / % possible all: 11.9

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→72.93 Å / SU ML: 0.3109 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 1186 2.99 %
Rwork0.2087 38434 -
obs0.2104 39620 60.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.79 Å2
Refinement stepCycle: LAST / Resolution: 2.18→72.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8366 0 246 194 8806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00168871
X-RAY DIFFRACTIONf_angle_d0.447612013
X-RAY DIFFRACTIONf_chiral_restr0.04211227
X-RAY DIFFRACTIONf_plane_restr0.00341536
X-RAY DIFFRACTIONf_dihedral_angle_d10.74483332
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.89469610891
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.899319047678
ens_2d_2DLX-RAY DIFFRACTIONTorsion NCS0.937830782811
ens_2d_3DLX-RAY DIFFRACTIONTorsion NCS0.829497394494
ens_3d_2ENX-RAY DIFFRACTIONTorsion NCS1.04899751215
ens_3d_3ENX-RAY DIFFRACTIONTorsion NCS1.04918739775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.280.327390.3076314X-RAY DIFFRACTION3.98
2.28-2.40.3123440.31921475X-RAY DIFFRACTION18.71
2.4-2.550.3879890.312906X-RAY DIFFRACTION36.73
2.55-2.740.39431380.29354254X-RAY DIFFRACTION53.8
2.74-3.020.33611810.2766070X-RAY DIFFRACTION76.43
3.02-3.450.27082150.22897165X-RAY DIFFRACTION89.63
3.45-4.350.25212510.1777909X-RAY DIFFRACTION98.01
4.35-72.930.2282590.18198341X-RAY DIFFRACTION99.84
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)
10.58714674563-0.2136619738270.4195806931030.0797932676563-0.08146516603291.57320162764-0.1942400879680.291093303720.220083271331-0.0478727431301-0.0925218312589-0.266163373734-0.2501796689760.846736041364-0.07095913949880.234323977772-0.1527858602490.1152222673620.4465310932430.06393552142110.53273806673538.544072013725.57485197510.9750860345
20.0266180056173-0.1843347794430.02110817486071.337201117220.1736107132030.4882320705540.06118808315220.267892346505-0.2002971221510.6987677214840.36423714999-0.5886707896790.0489212256676-0.3574853290050.1138669228440.4127966878460.0341828332994-0.07125233216870.6829613892080.01328296332610.72610371865636.129417135110.9132065137.1641085487
30.450872440084-0.007435828100060.2595777662040.843772894738-0.6699007167970.672021967964-0.00917930796604-0.3006996627970.1173849059320.5790441457230.00518422180353-0.406471080177-0.0214361751273-0.00715927767753-0.0001561736868990.4506128973840.0587235376712-0.07670381607660.375680432465-0.1115564958920.58349961001737.917114378114.493749001133.8682050024
42.45056452408-0.1512872489850.2713781545990.9025596218630.1149793805250.052323261368-0.177721948615-0.594983006514-0.2918795736980.3093651260040.334652949417-0.238132322216-0.224353296587-0.4146947086110.09529300495030.3274956513310.1500867355220.04803078929750.343138651608-0.1066898233550.152676270321.317806426725.558358811531.0011396615
52.380586062670.05173507164751.111045155871.090328775770.5483788684172.36918103698-0.0551822474942-7.80580903988E-5-0.1659154924910.05086571351990.0697891378252-0.0230945101793-0.0713700561586-0.01529064166770.0001492358611850.1832057130120.01865377067580.04064212366480.102785355661-0.02068024507340.30664684696419.503013039218.008081508314.6363456529
60.463794404081-0.5713135912820.07624198547321.51440901695-0.3619762324741.621137441350.0626811252063-0.2091396887920.147400043996-0.0173975078637-0.206668988961-0.0954610354952-0.558394804793-0.380308910781-0.00559297188560.3135537547090.03324855455560.02736240135750.269563900888-0.1302236895020.32326294185512.736065114532.280079379318.0395056224
73.801186692370.3550913836730.388801545030.5657168162150.4689423998050.673535625458-0.101016735005-0.5186546073370.0164220047661-0.00363154046276-0.09046667412920.1839084332850.136908175309-0.0809231565903-0.2658336919180.2304228984680.112204971404-0.00356486807424-0.00215569410163-0.1700056923070.4465018266641.17955137065-10.13111816890.108481001538
80.7432468562630.6566580915980.5467046693340.9206781315881.173833840552.33976477427-0.3998490718890.491253473038-0.0398621132557-0.4736220861660.2309816585160.3424342526040.5188925799410.307123711574-0.05089208074380.428570171477-0.0827628047047-0.1201381963150.335203624690.0735756619830.4237374085032.15200408178-19.4841108951-26.0329447693
92.089420518221.0044295131.247927907742.198757634091.09970923170.8826339671720.02849036357721.2867669114-0.340635353547-0.8619978858750.558092956584-0.4563684081690.02387004928620.4521203047690.3102871510540.597628921613-0.1237998201910.03120180861010.625597616268-0.05399818702130.30538131549518.3191604643-13.3123499277-25.8034150996
102.847218223130.2180941015610.2781169107291.79241071766-0.5239641734481.46062470524-0.05636065395740.258768652278-0.0281535561306-0.1779864611970.0440646992115-0.2339606770150.008603570578380.2855283271810.001374028345230.165133342356-0.0124951647723-0.0122043382742-0.00102627940331-0.03019666774720.36371705478821.3969564658-11.3807524579-6.74260891884
111.511135331980.01146180759270.6600956470770.7993801117940.07192675750962.210864077880.3219611939660.37537822057-0.04967395942310.00883014269603-0.06271225359050.2889843545480.0918932620338-0.03171172780990.1004899830270.2903008910650.144839574243-0.1160550235760.366777822367-0.1016341823890.0216136116435-1.2145291461147.7340995451-24.6638904085
123.480833065350.8214715922031.593205684780.4442582330050.4557457381020.7491370962850.1165824770290.599625011431-0.248450003895-0.552139703949-0.409707870691-0.586949015635-0.01340241350681.13888599479-0.1132103417280.5183438129230.1062965879180.1685299656740.9376036388540.1329472066470.49508628488315.174690168450.596880999-30.987067926
132.58851563497-0.2645388913811.821994377431.378084067540.1311390751882.46418815875-0.03552034474980.4566948765010.06641711663350.0383412766385-0.119792565164-0.216231324188-0.2687741666050.774038161183-0.02063680484460.297311180469-0.0687252880180.0248256400270.4154936246210.0009047941924830.11362934336818.839737737855.6242605437-12.4545888013
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 24 )AA2 - 241 - 23
22chain 'A' and (resid 25 through 58 )AA25 - 5824 - 57
33chain 'A' and (resid 59 through 108 )AA59 - 10858 - 107
44chain 'A' and (resid 109 through 149 )AA109 - 149108 - 148
55chain 'A' and (resid 150 through 280 )AA150 - 280149 - 279
66chain 'A' and (resid 281 through 331 )AA281 - 331280 - 330
77chain 'B' and (resid 1 through 24 )BD1 - 241 - 24
88chain 'B' and (resid 25 through 108 )BD25 - 10825 - 108
99chain 'B' and (resid 109 through 129 )BD109 - 129109 - 129
1010chain 'B' and (resid 130 through 331 )BD130 - 331130 - 331
1111chain 'C' and (resid 3 through 108 )CG3 - 1081 - 106
1212chain 'C' and (resid 109 through 129 )CG109 - 129107 - 127
1313chain 'C' and (resid 130 through 331 )CG130 - 331128 - 329

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