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- PDB-9r5f: Crystal structure of human protein kinase CK2 catalytic subunit (... -

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Basic information

Entry
Database: PDB / ID: 9r5f
TitleCrystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 5,6-dibromo-4,7-difluoro-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-4 / 7-difluoro-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
: / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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. / Lindenblatt, D. / Viht, K. / Uri, A. / Niefind, K.
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,3795
Polymers42,8801
Non-polymers4994
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint10 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.367, 47.779, 50.570
Angle α, β, γ (deg.)113.455, 90.205, 90.621
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-A1JCX / 5,6-bis(bromanyl)-4,7-bis(fluoranyl)-1~{H}-benzotriazole


Mass: 312.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6HBr2F2N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Reservoir: 900 mM LiCl, 100 mM TRIS-HCl pH 8.5, 28 % PEG6000 Protein/ligand mix: 5 mg per mL Ck2alpha Prime including 2 mM ligand and 10 % DMSO Drop: 2:1 mix of protein/ligand vs reservoir ...Details: Reservoir: 900 mM LiCl, 100 mM TRIS-HCl pH 8.5, 28 % PEG6000 Protein/ligand mix: 5 mg per mL Ck2alpha Prime including 2 mM ligand and 10 % DMSO Drop: 2:1 mix of protein/ligand vs reservoir optimization: Micro- and Macroseeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.19→46.552 Å / Num. obs: 82712 / % possible obs: 63.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 7.2 / Net I/σ(I): 10.3
Reflection shellResolution: 1.19→1.313 Å / Rmerge(I) obs: 1.096 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4136 / CC1/2: 0.374

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→32.93 Å / SU ML: 0.0814 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.9478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1547 4095 5.01 %
Rwork0.1265 77632 -
obs0.128 81727 64.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.2 Å2
Refinement stepCycle: LAST / Resolution: 1.19→32.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 25 444 3242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01352921
X-RAY DIFFRACTIONf_angle_d1.25633947
X-RAY DIFFRACTIONf_chiral_restr0.0999405
X-RAY DIFFRACTIONf_plane_restr0.0156506
X-RAY DIFFRACTIONf_dihedral_angle_d12.8971114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.210.276950.5188139X-RAY DIFFRACTION3.32
1.21-1.220.4113140.3565254X-RAY DIFFRACTION6.16
1.22-1.240.5723230.3504322X-RAY DIFFRACTION8.08
1.24-1.250.4919290.2984492X-RAY DIFFRACTION11.89
1.25-1.270.3141270.2894639X-RAY DIFFRACTION15.4
1.27-1.290.2621500.2389859X-RAY DIFFRACTION20.67
1.29-1.310.2985470.23381004X-RAY DIFFRACTION24.39
1.31-1.330.2719590.19841275X-RAY DIFFRACTION30.34
1.33-1.350.22640.18531522X-RAY DIFFRACTION36.42
1.35-1.370.23081120.17181868X-RAY DIFFRACTION45.4
1.37-1.40.22021140.15352342X-RAY DIFFRACTION56.25
1.4-1.430.2091290.14813165X-RAY DIFFRACTION76.02
1.43-1.460.19082120.14553632X-RAY DIFFRACTION87.05
1.46-1.490.19351580.13043823X-RAY DIFFRACTION91.62
1.49-1.520.17921950.12833805X-RAY DIFFRACTION91.93
1.52-1.560.16011740.12593845X-RAY DIFFRACTION92.28
1.56-1.60.14361980.1253835X-RAY DIFFRACTION92.27
1.6-1.650.16291560.12673877X-RAY DIFFRACTION92.01
1.65-1.70.14781930.10833824X-RAY DIFFRACTION92.28
1.7-1.760.16542060.10753787X-RAY DIFFRACTION91.52
1.76-1.830.15542140.10523743X-RAY DIFFRACTION91.32
1.83-1.920.14372650.09933736X-RAY DIFFRACTION90.87
1.92-2.020.12862110.10043711X-RAY DIFFRACTION89.89
2.02-2.140.12511960.09933616X-RAY DIFFRACTION87.77
2.14-2.310.11682130.10463389X-RAY DIFFRACTION82.2
2.31-2.540.14281750.11333325X-RAY DIFFRACTION80.15
2.54-2.910.14552290.12564015X-RAY DIFFRACTION97.72
2.91-3.670.14812290.12834040X-RAY DIFFRACTION97.67
3.67-32.930.17361980.16143748X-RAY DIFFRACTION90.38

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