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- PDB-6te2: Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene... -

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Basic information

Entry
Database: PDB / ID: 6te2
TitleCrystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the 2-aminothiazole-type inhibitor 17
ComponentsCasein kinase II subunit alpha'Casein kinase 2
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / ATP-competitive inhibitor / 2-aminothiazole derivative
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 / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / acrosomal vesicle / Signal transduction by L1 / liver regeneration / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / spermatogenesis / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 ...Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-N4N / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.922 Å
AuthorsNiefind, K. / Lindenblatt, D. / Jose, J. / Applegate, V.M. / Nickelsen, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNI 643/4-2 Germany
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural and Mechanistic Basis of the Inhibitory Potency of Selected 2-Aminothiazole Compounds on Protein Kinase CK2.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Jose, J. / Niefind, K.
History
DepositionNov 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _software.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,1772
Polymers42,8801
Non-polymers2971
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.339, 47.493, 50.357
Angle α, β, γ (deg.)66.812, 89.925, 88.974
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' / Casein kinase 2 / 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-N4N / 3-[(4-pyridin-2-yl-1,3-thiazol-2-yl)amino]benzoic acid


Mass: 297.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpja' (mutant Cys336Ser) ...Details: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpja' (mutant Cys336Ser) /inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha-'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the 2-aminothiazole-type inhibitor 17 by extensive crystal soaking.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.922→32.074 Å / Num. obs: 206560 / % possible obs: 76 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.021 / Rrim(I) all: 0.042 / Rsym value: 0.036 / Net I/σ(I): 14.9
Reflection shellResolution: 0.922→0.976 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10328 / CC1/2: 0.541 / Rpim(I) all: 0.55 / Rrim(I) all: 1.079 / Rsym value: 0.927 / % possible all: 24.5

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Processing

Software
NameVersionClassification
XDSdata reduction
autoPROCdata scaling
Arcimboldophasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.922→32.07 Å / SU ML: 0.0501 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 15.1397
RfactorNum. reflection% reflection
Rfree0.1463 2032 0.98 %
Rwork0.1276 --
obs0.1278 206560 74.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.48 Å2
Refinement stepCycle: LAST / Resolution: 0.922→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 21 439 3219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01662966
X-RAY DIFFRACTIONf_angle_d1.39974017
X-RAY DIFFRACTIONf_chiral_restr0.1138408
X-RAY DIFFRACTIONf_plane_restr0.0113522
X-RAY DIFFRACTIONf_dihedral_angle_d16.39451137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.91-0.940.186680.28713X-RAY DIFFRACTION3.9
0.94-0.960.2202390.25964484X-RAY DIFFRACTION24.28
0.96-0.980.276890.2428272X-RAY DIFFRACTION44.76
0.98-1.010.23791200.226911955X-RAY DIFFRACTION64.87
1.01-1.050.22441380.204214800X-RAY DIFFRACTION80.37
1.05-1.080.18431500.175414950X-RAY DIFFRACTION81.12
1.08-1.130.1591670.137916529X-RAY DIFFRACTION89.69
1.13-1.180.14621630.117716560X-RAY DIFFRACTION89.77
1.18-1.240.16151570.108816531X-RAY DIFFRACTION89.56
1.24-1.320.12371820.102816245X-RAY DIFFRACTION87.93
1.32-1.420.11541530.101215499X-RAY DIFFRACTION84.32
1.42-1.560.10721620.098317166X-RAY DIFFRACTION93.15
1.56-1.790.1181740.103817121X-RAY DIFFRACTION92.77
1.79-2.250.1251630.117616578X-RAY DIFFRACTION89.98
2.25-32.070.16071670.136417235X-RAY DIFFRACTION93.41

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