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- PDB-7x4h: Crystal structure of CK2a1 complexed with AG1112 -

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Basic information

Entry
Database: PDB / ID: 7x4h
TitleCrystal structure of CK2a1 complexed with AG1112
ComponentsCasein Kinase 2 subunit alpha
KeywordsTRANSFERASE / protein kinase
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
Chem-8BH / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsIkeda, A. / Kinoshita, T. / Tsuyuguchi, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Bivalent binding mode of an amino-pyrazole inhibitor indicates the potentials for CK2 alpha 1-selective inhibitors.
Authors: Ikeda, A. / Tsuyuguchi, M. / Kitagawa, D. / Sawa, M. / Nakamura, S. / Nakanishi, I. / Kinoshita, T.
History
DepositionMar 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Casein Kinase 2 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0273
Polymers40,4781
Non-polymers5492
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint14 kcal/mol
Surface area16450 Å2
Unit cell
Length a, b, c (Å)48.025, 79.377, 82.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Casein Kinase 2 subunit alpha


Mass: 40478.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-8BH / 5-azanyl-3-[(~{Z})-1-cyano-2-(1~{H}-indol-3-yl)ethenyl]-1~{H}-pyrazole-4-carbonitrile / Tyrphostin AG 1112


Mass: 274.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.94 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2017
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 31204 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 11.84 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.143 / Net I/σ(I): 30.7
Reflection shellResolution: 1.77→1.8 Å / Num. unique obs: 1537 / CC1/2: 0.853

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAR

3war


Resolution: 1.77→41.47 Å / SU ML: 0.1639 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.6602 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2076 1991 6.39 %
Rwork0.1686 29147 -
obs0.1711 31138 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.14 Å2
Refinement stepCycle: LAST / Resolution: 1.77→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 66 329 3212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762957
X-RAY DIFFRACTIONf_angle_d1.05163986
X-RAY DIFFRACTIONf_chiral_restr0.0557405
X-RAY DIFFRACTIONf_plane_restr0.0049511
X-RAY DIFFRACTIONf_dihedral_angle_d28.99561108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.820.26341350.1961971X-RAY DIFFRACTION96.69
1.82-1.870.21361450.17712064X-RAY DIFFRACTION99.77
1.87-1.920.20671400.16532033X-RAY DIFFRACTION99.77
1.92-1.980.19451410.16612066X-RAY DIFFRACTION100
1.98-2.050.2231360.15852053X-RAY DIFFRACTION100
2.05-2.140.18521470.15662053X-RAY DIFFRACTION100
2.14-2.230.1781400.15832079X-RAY DIFFRACTION99.95
2.23-2.350.19951350.1642081X-RAY DIFFRACTION99.95
2.35-2.50.23411450.16732075X-RAY DIFFRACTION100
2.5-2.690.25381430.17752082X-RAY DIFFRACTION100
2.69-2.960.21131380.1842107X-RAY DIFFRACTION100
2.96-3.390.20651470.17722103X-RAY DIFFRACTION100
3.39-4.270.19521520.15142135X-RAY DIFFRACTION99.96
4.27-41.470.19591470.17522245X-RAY DIFFRACTION99.67

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