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- PDB-9r57: Crystal structure of human protein kinase CK2 catalytic subunit (... -

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Basic information

Entry
Database: PDB / ID: 9r57
TitleCrystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 5,6-dibromo-1H-1,2,3-benzotriazole
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / human protein kinase CK2 / human casein kinase 2 / isoenzyme ck2alpha' / CSNK2A2 / 5 / 6-dibromo-1H-1 / 2 / 3-benzotriazole
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
5,6-DIBROMOBENZOTRIAZOLE / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsKasperowicz, S. / Werner, C. / Podsiadla-Bialoskorska, M. / Szolajska, E. / Lindenblatt, D. / Niefind, K. / Poznanski, J. / Winiewska-Szajewska, M.
Funding support Germany, Poland, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
Polish National Science Centre2022/45/N/ST4/02628 Poland
Citation
Journal: Bioorg.Chem. / Year: 2025
Title: Novel fluoro-brominated benzotriazoles as potential CK2 inhibitors. How does fluorination affect the properties of benzotriazoles?
Authors: Kasperowicz, S. / Werner, C. / Podsiadla-Bialoskorska, M. / Szolajska, E. / Maciejewska, A.M. / Lindenblatt, D. / Niefind, K. / Poznanski, J. / Winiewska-Szajewska, M.
#1: Journal: To Be Published
Title: Discovery and Exploration of Protein Kinase CK2 Binding Sites Using CK2alpha'Cys336Ser as an Exquisite Crystallographic Tool
Authors: Werner, C.
History
DepositionMay 8, 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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2193
Polymers42,8801
Non-polymers3392
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint3 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.109, 47.423, 50.453
Angle α, β, γ (deg.)113.193, 90.233, 91.300
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: 42879.867 Da / Num. of mol.: 1
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-7M0 / 5,6-DIBROMOBENZOTRIAZOLE / DIBROMO-2-BENZOTRIAZOLE


Mass: 276.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3Br2N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 900 mM LiCl, 100 mM TRIS-HCl pH 8.5, 28 % PEG6000 Inititial drop: 5 mg per mL CK2alpha Prime with 1 mM MB002, 10 percent DMSO mixed in 2:1 ratio with reservoir (10 and 5 ...Details: Reservoir: 900 mM LiCl, 100 mM TRIS-HCl pH 8.5, 28 % PEG6000 Inititial drop: 5 mg per mL CK2alpha Prime with 1 mM MB002, 10 percent DMSO mixed in 2:1 ratio with reservoir (10 and 5 microliter). Optimization of crystal by microseeding and macroseeding. Complex formation by extensive purging with reservoir solution and extensive soaking at compounds saturation limit.

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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 CdTe 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.095→46.371 Å / Num. obs: 129390 / % possible obs: 80 % / Redundancy: 2.2 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.067 / Net I/σ(I): 4.4
Reflection shellResolution: 1.095→1.156 Å / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6470 / CC1/2: 0.533

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→23.63 Å / SU ML: 0.0663 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 15.3383
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.15 6210 4.8 %
Rwork0.1301 123125 -
obs0.1311 129335 80.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.65 Å2
Refinement stepCycle: LAST / Resolution: 1.1→23.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 15 374 3157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01922904
X-RAY DIFFRACTIONf_angle_d1.43333924
X-RAY DIFFRACTIONf_chiral_restr0.1265404
X-RAY DIFFRACTIONf_plane_restr0.0216503
X-RAY DIFFRACTIONf_dihedral_angle_d13.29441115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.2462270.2289564X-RAY DIFFRACTION11.04
1.11-1.120.2681460.2074901X-RAY DIFFRACTION17.57
1.12-1.130.1985660.20181304X-RAY DIFFRACTION25.54
1.13-1.150.2697930.20742064X-RAY DIFFRACTION39.92
1.15-1.160.23551310.19672747X-RAY DIFFRACTION54.06
1.16-1.180.21740.18353596X-RAY DIFFRACTION68.97
1.18-1.20.20931900.17643998X-RAY DIFFRACTION77.99
1.2-1.210.18782230.17224299X-RAY DIFFRACTION83.14
1.21-1.230.18242510.17364301X-RAY DIFFRACTION85.9
1.23-1.250.15682410.16584466X-RAY DIFFRACTION87.04
1.25-1.280.18942090.16254577X-RAY DIFFRACTION88.38
1.28-1.30.18832330.15054567X-RAY DIFFRACTION89.75
1.3-1.320.17832300.14284662X-RAY DIFFRACTION90.14
1.32-1.350.19051970.14264657X-RAY DIFFRACTION90.27
1.35-1.380.16131650.13984679X-RAY DIFFRACTION90.37
1.38-1.410.13832110.12684737X-RAY DIFFRACTION91.29
1.41-1.450.14522170.12074743X-RAY DIFFRACTION92.38
1.45-1.490.14292160.11754861X-RAY DIFFRACTION93.21
1.49-1.530.14582600.10924769X-RAY DIFFRACTION93.62
1.53-1.580.1382610.1044765X-RAY DIFFRACTION93.52
1.58-1.640.13382810.10434804X-RAY DIFFRACTION93.51
1.64-1.70.12132550.10474738X-RAY DIFFRACTION93.85
1.7-1.780.12522400.10674767X-RAY DIFFRACTION93.34
1.78-1.870.12982700.10864680X-RAY DIFFRACTION91.68
1.87-1.990.12012600.10644768X-RAY DIFFRACTION92.94
1.99-2.140.11992610.10594842X-RAY DIFFRACTION94.82
2.14-2.360.12862730.11084873X-RAY DIFFRACTION95.49
2.36-2.70.14543080.11914848X-RAY DIFFRACTION95.55
2.7-3.40.14852370.1374806X-RAY DIFFRACTION93.44
3.4-23.630.19051840.15784742X-RAY DIFFRACTION91.6

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