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- PDB-7xyh: Crystal structure of CK2a2 complexed with AG1112 -

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Basic information

Entry
Database: PDB / ID: 7xyh
TitleCrystal structure of CK2a2 complexed with AG1112
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase
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 / Maturation of hRSV A proteins ...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 / Maturation of hRSV A proteins / negative regulation of apoptotic signaling pathway / negative regulation of proteasomal 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 / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / 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 / 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: 2.04 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
DepositionJun 1, 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 II subunit alpha'
B: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,61316
Polymers80,3202
Non-polymers1,29314
Water2,954164
1
A: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8699
Polymers40,1601
Non-polymers7098
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7457
Polymers40,1601
Non-polymers5856
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.555, 62.541, 74.065
Angle α, β, γ (deg.)81.424, 75.370, 72.005
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' / CK II alpha'


Mass: 40159.984 Da / Num. of mol.: 2
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-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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 10000, Tris-HCl pH 8.0, Sucrose

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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 EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.04→47.47 Å / Num. obs: 47685 / % possible obs: 97.1 % / Redundancy: 3.64 % / Biso Wilson estimate: 33.55 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.144 / Net I/σ(I): 6.79
Reflection shellResolution: 2.04→2.16 Å / Num. unique obs: 7550 / CC1/2: 0.474

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TEW

6tew


Resolution: 2.04→35.72 Å / SU ML: 0.3344 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.4832 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2822 2381 5 %
Rwork0.231 45266 -
obs0.2336 47647 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.23 Å2
Refinement stepCycle: LAST / Resolution: 2.04→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 90 164 5752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01555722
X-RAY DIFFRACTIONf_angle_d1.46377702
X-RAY DIFFRACTIONf_chiral_restr0.0599792
X-RAY DIFFRACTIONf_plane_restr0.0087980
X-RAY DIFFRACTIONf_dihedral_angle_d20.5122162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.080.37211340.36522540X-RAY DIFFRACTION93.17
2.08-2.120.34151390.34052639X-RAY DIFFRACTION96.12
2.12-2.170.40181400.33092656X-RAY DIFFRACTION96.65
2.17-2.230.36011370.33062629X-RAY DIFFRACTION96.08
2.23-2.290.3541390.31012641X-RAY DIFFRACTION96.53
2.29-2.350.36861400.31012670X-RAY DIFFRACTION96.53
2.35-2.430.32731400.28852668X-RAY DIFFRACTION97.06
2.43-2.520.34851410.28252676X-RAY DIFFRACTION97.85
2.52-2.620.34771420.28212698X-RAY DIFFRACTION98.03
2.62-2.740.32781430.26622706X-RAY DIFFRACTION98
2.74-2.880.30321400.2592677X-RAY DIFFRACTION98.02
2.88-3.060.32971420.24582697X-RAY DIFFRACTION98.27
3.06-3.30.32271410.24332677X-RAY DIFFRACTION97.68
3.3-3.630.2961420.21292692X-RAY DIFFRACTION97.96
3.63-4.150.25991400.1822656X-RAY DIFFRACTION96.92
4.15-5.230.18961400.16432659X-RAY DIFFRACTION96.92
5.23-35.720.19091410.17592685X-RAY DIFFRACTION97.65

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