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- PDB-9r5d: Crystal structure of human protein kinase CK2 catalytic subunit (... -

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Basic information

Entry
Database: PDB / ID: 9r5d
TitleCrystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 4,6-dibromo-5,7-difluoro-1H-1,2,3-benzotriazole
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / human protein kinase CK2 / human casein kinase 2 / isoenzyme ck2alpha' / CSNK2A2 / 4 / 6-dibromo-5 / 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: 1.02 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,5037
Polymers42,8801
Non-polymers6236
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint15 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.629, 48.013, 50.942
Angle α, β, γ (deg.)113.309, 89.993, 90.826
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1JC0 / 4,6-bis(bromanyl)-5,7-bis(fluoranyl)-1~{H}-benzotriazole


Mass: 312.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6HBr2F2N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Reservoir was: 900 mM LiCl, 100 mM TRIS-HCl pH 8.5, 28 % PEG6000. Protein/Ligand mix: 5 mg per mL CK2alpha Prime mixed with 2 mM ligand and 10 % DMSO. Drop: 2:1 mix of protein and ligand vs ...Details: Reservoir was: 900 mM LiCl, 100 mM TRIS-HCl pH 8.5, 28 % PEG6000. Protein/Ligand mix: 5 mg per mL CK2alpha Prime mixed with 2 mM ligand and 10 % DMSO. Drop: 2:1 mix of protein and ligand vs resevoir Optimization: Micro- and macroseeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.02→46.623 Å / Num. obs: 147987 / % possible obs: 71.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 18.33 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.078 / Rrim(I) all: 0.194 / Rsym value: 0.177 / Net I/σ(I): 11.7
Reflection shellResolution: 1.02→1.129 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.228 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7399 / CC1/2: 0.131 / Rpim(I) all: 0.728 / Rrim(I) all: 1.438 / Rsym value: 1.228 / % possible all: 13.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.02→46.62 Å / SU ML: 0.1185 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.8691
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1927 7312 4.96 %
Rwork0.1711 140152 -
obs0.1721 147464 71.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.23 Å2
Refinement stepCycle: LAST / Resolution: 1.02→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 33 237 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01222972
X-RAY DIFFRACTIONf_angle_d1.15644020
X-RAY DIFFRACTIONf_chiral_restr0.0919412
X-RAY DIFFRACTIONf_plane_restr0.0139518
X-RAY DIFFRACTIONf_dihedral_angle_d13.1221133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.030.574420.702653X-RAY DIFFRACTION0.8
1.03-1.040.624290.6178X-RAY DIFFRACTION2.74
1.04-1.060.5426200.5329323X-RAY DIFFRACTION5.03
1.06-1.070.5223240.4667569X-RAY DIFFRACTION8.6
1.07-1.080.4107420.4095865X-RAY DIFFRACTION13.13
1.08-1.10.426520.35841235X-RAY DIFFRACTION18.79
1.1-1.110.3274820.32471739X-RAY DIFFRACTION26.47
1.11-1.130.31891030.3192603X-RAY DIFFRACTION39.08
1.13-1.150.33121580.29073637X-RAY DIFFRACTION55.74
1.15-1.170.29852430.27644665X-RAY DIFFRACTION70.63
1.17-1.190.28922820.26185181X-RAY DIFFRACTION79.95
1.19-1.210.28752910.25615551X-RAY DIFFRACTION84.97
1.21-1.230.29162560.24785860X-RAY DIFFRACTION88.41
1.23-1.260.2733080.23075888X-RAY DIFFRACTION90.72
1.26-1.290.25363080.22496007X-RAY DIFFRACTION92.55
1.29-1.320.24213090.21336164X-RAY DIFFRACTION93.62
1.32-1.350.27983170.22626219X-RAY DIFFRACTION94.64
1.35-1.380.25133330.1996192X-RAY DIFFRACTION94.69
1.38-1.430.20413720.16866256X-RAY DIFFRACTION96.76
1.43-1.470.17983840.15616371X-RAY DIFFRACTION97.45
1.47-1.520.19893750.14686308X-RAY DIFFRACTION98.05
1.52-1.590.16894400.14556393X-RAY DIFFRACTION98.6
1.59-1.660.16163340.14196491X-RAY DIFFRACTION99.01
1.66-1.740.16742860.13416501X-RAY DIFFRACTION98.94
1.74-1.850.16123220.13726361X-RAY DIFFRACTION97.08
1.85-20.15833110.13216549X-RAY DIFFRACTION99.9
2-2.20.13112730.13136626X-RAY DIFFRACTION99.99
2.2-2.520.16723820.13526467X-RAY DIFFRACTION99.93
2.52-3.170.16873600.15586509X-RAY DIFFRACTION99.26
3.17-46.620.1683340.16356391X-RAY DIFFRACTION97.95

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