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- PDB-7qgc: H. SAPIENS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPE... -

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Entry
Database: PDB / ID: 7qgc
TitleH. SAPIENS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 5,6-DIBROMOBENZOTRIAZOLE AT PH 5.5
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2 / CASEIN KINASE 2 / INHIBITOR / BROMO-BENZOTRIAZOLE / HALOGEN BOND / TRANSFERASE-INHIBITOR COMPLEX
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 / Maturation of hRSV A proteins ...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 / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / 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
5,6-DIBROMOBENZOTRIAZOLE / CITRATE ANION / DI(HYDROXYETHYL)ETHER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWiniewska-Szajewska, M. / Czapinska, H. / Kaus-Drobek, M. / Piasecka, A. / Mieczkowska, K. / Dadlez, M. / Bochtler, M. / Poznanski, J.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
Polish National Science Centre2012/07/B/ST4/01334European Union
Polish National Science Centre2017/25/B/ST4/01613European Union
European Communitys Seventh Framework Programme283570European Union
Citation
Journal: Sci Rep / Year: 2022
Title: Competition between electrostatic interactions and halogen bonding in the protein-ligand system: structural and thermodynamic studies of 5,6-dibromobenzotriazole-hCK2 alpha complexes.
Authors: Winiewska-Szajewska, M. / Czapinska, H. / Kaus-Drobek, M. / Fricke, A. / Mieczkowska, K. / Dadlez, M. / Bochtler, M. / Poznanski, J.
#1: Journal: J Phys Chem B / Year: 2021
Title: Halogen Atoms in the Protein-Ligand System. Structural and Thermodynamic Studies of the Binding of Bromobenzotriazoles by the Catalytic Subunit of Human Protein Kinase CK2.
Authors: Czapinska, H. / Winiewska-Szajewska, M. / Szymaniec-Rutkowska, A. / Piasecka, A. / Bochtler, M. / Poznanski, J.
#2: Journal: Biochim Biophys Acta / Year: 2015
Title: Thermodynamics parameters for binding of halogenated benzotriazole inhibitors of human protein kinase CK2alpha.
Authors: Winiewska, M. / Kucinska, K. / Makowska, M. / Poznanski, J. / Shugar, D.
#3: Journal: Biochem Biophys Res Commun / Year: 2015
Title: Thermodynamic parameters for binding of some halogenated inhibitors of human protein kinase CK2.
Authors: Winiewska, M. / Makowska, M. / Maj, P. / Wielechowska, M. / Bretner, M. / Poznanski, J. / Shugar, D.
#4: Journal: IUBMB Life / Year: 2020
Title: A competition between hydrophobic and electrostatic interactions in protein-ligand systems. Binding of heterogeneously halogenated benzotriazoles by the catalytic subunit of human protein kinase CK2.
Authors: Kasperowicz, S. / Marzec, E. / Maciejewska, A.M. / Trzybinski, D. / Bretner, M. / Wozniak, K. / Poznanski, J. / Mieczkowska, K.
History
DepositionDec 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8524
Polymers46,2801
Non-polymers5723
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.472, 127.472, 60.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-596-

HOH

21A-624-

HOH

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Components

#1: Protein Casein kinase II subunit alpha / CK II alpha


Mass: 46279.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: PET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, 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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 20% polyethylene glycol 550 ...Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 20% polyethylene glycol 550 monomethyl ester, 10% polyethylene glycol 20 000, and 0.1 M buffering solution of imidazole/MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9117 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9117 Å / Relative weight: 1
ReflectionResolution: 2.55→45.1 Å / Num. obs: 16932 / % possible obs: 99.9 % / Redundancy: 26.26 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.304 / Rsym value: 0.298 / Net I/σ(I): 10.68
Reflection shellResolution: 2.55→2.7 Å / Redundancy: 26.93 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2658 / CC1/2: 0.8 / Rrim(I) all: 1.359 / Rsym value: 1.334 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREPphasing
ARP/wARPmodel building
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAR

3war


Resolution: 2.55→45.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.531 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.541 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE SOLVENT MOLECULE IDENTITIES AND RELATIVE OCCUPANCIES OF STATICALLY DISORDERED RESIDUES HAVE BEEN ...Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE SOLVENT MOLECULE IDENTITIES AND RELATIVE OCCUPANCIES OF STATICALLY DISORDERED RESIDUES HAVE BEEN ASSIGNED TENTATIVELY. THERE ARE A FEW DENSITY CLUSTERS THAT MAY CORRESPOND TO SOLVENT MOLECULES BUT UNAMBIGUOUS DISTINCTION BETWEEN VARIOUS BUFFER COMPONENTS WAS NOT STRAIGHTFORWARD AND THUS THE WATER MOLECULES WERE RETAINED IN THE FINAL MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 839 5 %THIN RESOLUTION SHELLS
Rwork0.1705 ---
obs0.1735 16093 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.04 Å2 / Biso mean: 42.542 Å2 / Biso min: 14.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-0 Å2
2--0.85 Å2-0 Å2
3----1.71 Å2
Refinement stepCycle: final / Resolution: 2.55→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 31 330 3173
Biso mean--62.51 44.25 -
Num. residues----333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193215
X-RAY DIFFRACTIONr_bond_other_d0.0020.023019
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9554368
X-RAY DIFFRACTIONr_angle_other_deg0.86236948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85322.914175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96215582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4781532
X-RAY DIFFRACTIONr_chiral_restr0.0710.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023706
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02816
LS refinement shellResolution: 2.55→2.615 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.332 48 -
Rwork0.292 1158 -
obs--99.67 %

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