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- PDB-7at9: Structure of protein kinase ck2 catalytic subunit (csnk2a2 gene p... -

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Basic information

Entry
Database: PDB / ID: 7at9
TitleStructure of protein kinase ck2 catalytic subunit (csnk2a2 gene product) in complex with the ATP-competitive inhibitor MB002 and the alphaD-pocket ligand 3,4-dichlorophenethylamine
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / bivalent inhibitor
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of mitophagy / regulation of chromosome separation / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / acrosomal vesicle / liver regeneration / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / 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
2-(3,4-dichlorophenyl)ethanamine / Chem-4B0 / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.05 Å
AuthorsLindenblatt, D. / Applegate, V. / Nickelsen, A. / Klussmann, M. / Neundorf, I. / Goetz, C. / Jose, J. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/4-2 Germany
Citation
Journal: J.Med.Chem. / Year: 2022
Title: Molecular Plasticity of Crystalline CK2 alpha ' Leads to KN2, a Bivalent Inhibitor of Protein Kinase CK2 with Extraordinary Selectivity.
Authors: Lindenblatt, D. / Applegate, V. / Nickelsen, A. / Klussmann, M. / Neundorf, I. / Gotz, C. / Jose, J. / Niefind, K.
#1: Journal: ACS Omega / Year: 2019
Title: Diacritic Binding of an Indenoindole Inhibitor by CK2alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2alpha' Structures
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Hochscherf, J. / Witulski, B. / Bouaziz, Z. / Marminon, C. / Bretner, M. / Le Borgne, M. / Jose, J. / Niefind, K.
#2: Journal: 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
DepositionOct 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)44,30415
Polymers42,8801
Non-polymers1,42414
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-20 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.482, 47.661, 50.733
Angle α, β, γ (deg.)66.614, 89.437, 88.659
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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: 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

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Non-polymers , 6 types, 404 molecules

#2: Chemical ChemComp-42J / 2-(3,4-dichlorophenyl)ethanamine


Mass: 190.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9Cl2N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-4B0 / 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol


Mass: 492.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7Br4N3O
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
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 CK2alpha' (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 CK2alpha' (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 alphaD-pocket ligand 3,4-dichlorophenethylamine was introduced by extensive soaking.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873127 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873127 Å / Relative weight: 1
ReflectionResolution: 1.039→46.565 Å / Num. obs: 154027 / % possible obs: 80.1 % / Redundancy: 8.6 % / Biso Wilson estimate: 11.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.025 / Rrim(I) all: 0.079 / Rsym value: 0.075 / Net I/σ(I): 13.4
Reflection shellResolution: 1.039→1.103 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.096 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7703 / CC1/2: 0.513 / Rpim(I) all: 0.558 / Rrim(I) all: 1.239 / Rsym value: 1.096 / % possible all: 24.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
PHENIXmodel building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.05→43.74 Å / SU ML: 0.0837 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.242
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1496 1555 1.01 %
Rwork0.1291 152249 -
obs0.1293 153804 81.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.12 Å2
Refinement stepCycle: LAST / Resolution: 1.05→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 71 390 3225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01023108
X-RAY DIFFRACTIONf_angle_d1.16334214
X-RAY DIFFRACTIONf_chiral_restr0.0931425
X-RAY DIFFRACTIONf_plane_restr0.0089544
X-RAY DIFFRACTIONf_dihedral_angle_d17.4711216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.080.3102340.27033218X-RAY DIFFRACTION18.79
1.08-1.120.208750.22717002X-RAY DIFFRACTION41.41
1.12-1.160.2053960.191210485X-RAY DIFFRACTION61.13
1.16-1.210.21621460.168413518X-RAY DIFFRACTION79.79
1.21-1.280.1781650.144316525X-RAY DIFFRACTION97
1.28-1.360.151760.11816768X-RAY DIFFRACTION98.33
1.36-1.460.15081740.101816834X-RAY DIFFRACTION98.77
1.46-1.610.11471730.096816885X-RAY DIFFRACTION99.21
1.61-1.840.13071710.103216950X-RAY DIFFRACTION99.55
1.84-2.320.13231700.119217043X-RAY DIFFRACTION99.91
2.32-43.740.15581750.141817021X-RAY DIFFRACTION99.98

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