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- PDB-6tll: HUMAN CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIV... -

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Basic information

Entry
Database: PDB / ID: 6tll
TitleHUMAN CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 4,5,6,7-TETRABROMOBENZOTRIAZOLE (tBBT)
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2 / CASEIN KINASE 2 / INHIBITOR / BROMO-BENZOTRIAZOLE / HALOGEN BOND / TRANSFERASE-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 / Sin3-type complex / Synthesis of PC / 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 / Sin3-type complex / 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 / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / 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
DI(HYDROXYETHYL)ETHER / 4,5,6,7-TETRABROMOBENZOTRIAZOLE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsCzapinska, H. / Piasecka, A. / Winiewska-Szajewska, M. / Bochtler, M. / Poznanski, J.
Funding support Poland, 3items
OrganizationGrant numberCountry
Polish National Science Centre2012/07/B/ST4/01334 Poland
Polish National Science Centre2017/25/B/ST4/01613 Poland
European Communitys Seventh Framework Programme283570
Citation
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.
#1: Journal: Biochim. Biophys. Acta / Year: 2015
Title: Thermodynamics parameters for binding of halogenated benzotriazole inhibitors of human protein kinase CK2 alpha.
Authors: Winiewska, M. / Kucinska, K. / Makowska, M. / Poznanski, J. / Shugar, D.
#2: 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.
History
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)47,4558
Polymers46,2801
Non-polymers1,1767
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-21 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.431, 127.431, 61.031
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-739-

HOH

21A-805-

HOH

31A-867-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 442 molecules

#2: Chemical ChemComp-TBS / 4,5,6,7-TETRABROMOBENZOTRIAZOLE / TETRABROMO-2-BENZOTRIAZOLE


Mass: 434.708 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6HBr4N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 7.5
Details: 0.1 M sodium HEPES/MOPS buffer pH 7.5, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium ...Details: 0.1 M sodium HEPES/MOPS buffer pH 7.5, 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 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9116 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.88→45.1 Å / Num. obs: 41198 / % possible obs: 99.6 % / Redundancy: 24.8 % / Biso Wilson estimate: 46.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.091 / Rsym value: 0.089 / Net I/σ(I): 20.57
Reflection shellResolution: 1.88→1.99 Å / Redundancy: 23.6 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 6414 / CC1/2: 0.851 / Rrim(I) all: 1.278 / Rsym value: 1.251 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
ARP/wARPmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAR

3war


Resolution: 1.88→45.05 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.466 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.112
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED HAVE BEEN REPORTED. THE RELATIVE OCCUPANCIES OF THE LIGAND POSES AND STATICALLY DISORDERED RESIDUES HAVE BEEN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED HAVE BEEN REPORTED. THE RELATIVE OCCUPANCIES OF THE LIGAND POSES AND STATICALLY DISORDERED RESIDUES HAVE BEEN ASSIGNED TENTATIVELY. THE RADIATION DAMAGE TRIGGERED COVALENT BOND BETWEEN THE SECOND LIGAND MOLECULE (AWAY FROM THE ACTIVE SITE) AND THE PROTEIN WAS CONSIDERED BUT NOT BUILT. THE DENSITY NEXT TO THE SIDE CHAIN OF TYR257 MAY CORRESPOND TO PARTIAL OXIDATION DUE TO XRAY RADIATION BUT SINCE THE EFFECT IS LIKELY TO BE AN ARTIFACT OF THE EXPERIMENTAL METHOD, IT WAS NOT MODELLED. THE ION IDENTITIES HAVE BEEN ASSIGNED TENTATIVELY. THERE ARE A FEW WATER 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
Rfree0.187 2038 4.9 %RANDOM
Rwork0.1597 ---
obs0.161 39160 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.88 Å2 / Biso mean: 46.177 Å2 / Biso min: 16.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å2-0 Å2
2--0.63 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: final / Resolution: 1.88→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 82 435 3329
Biso mean--75.01 60.94 -
Num. residues----333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133475
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173100
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.6544740
X-RAY DIFFRACTIONr_angle_other_deg1.2451.5867210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.09521.182220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00615624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4141533
X-RAY DIFFRACTIONr_chiral_restr0.060.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024018
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02802
LS refinement shellResolution: 1.881→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 93 -
Rwork0.315 2759 -
all-2852 -
obs--94.85 %
Refinement TLS params.Method: refined / Origin x: 54.8516 Å / Origin y: 22.2049 Å / Origin z: 21.9526 Å
111213212223313233
T0.1148 Å2-0.062 Å2-0.0199 Å2-0.0881 Å20.0097 Å2--0.0127 Å2
L2.4478 °2-0.6606 °2-0.6746 °2-0.91 °20.145 °2--1.2241 °2
S0.0334 Å °-0.2326 Å °-0.0056 Å °-0.047 Å °0.0652 Å °-0.012 Å °0.0294 Å °0.0793 Å °-0.0986 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 334
2X-RAY DIFFRACTION1I1 - 10
3X-RAY DIFFRACTION1W1 - 800

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