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- PDB-4gub: Casein Kinase II bound to Inhibitor -

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Basic information

Entry
Database: PDB / ID: 4gub
TitleCasein Kinase II bound to Inhibitor
ComponentsCasein kinase II subunit alpha
KeywordsTransferase/transferase inhibitor / kinase / transferase / cytosol / 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 / Maturation of hRSV A proteins ...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 / 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 / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / regulation of cell cycle / non-specific serine/threonine protein kinase / negative regulation of translation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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-0Y4 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLarsen, N.A. / Dowling, J.E.
CitationJournal: To be Published
Title: Potent and selective inhibitors of CK2 kinase.
Authors: Dowling, J.E. / Larsen, N.A.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)40,3153
Polymers39,8781
Non-polymers4372
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.637, 141.728, 49.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Casein kinase II subunit alpha / CK II alpha


Mass: 39878.496 Da / Num. of mol.: 1 / Fragment: subunit alpha
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-0Y4 / N-[5-({3-cyano-7-[(1-methyl-1H-imidazol-4-yl)amino]pyrazolo[1,5-a]pyrimidin-5-yl}amino)-2-methylphenyl]acetamide


Mass: 401.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N9O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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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: 3.39 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22-26% PEG 6K, 200 mM ammonium sulfate, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→77.6 Å / Num. all: 27897 / Num. obs: 27864 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 22.91 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2631 / % possible all: 91.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→18.49 Å / Cor.coef. Fo:Fc: 0.8948 / Cor.coef. Fo:Fc free: 0.8571 / SU R Cruickshank DPI: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 1401 5.05 %RANDOM
Rwork0.1982 ---
obs0.2002 27755 98.23 %-
all-27755 --
Displacement parametersBiso mean: 28.99 Å2
Baniso -1Baniso -2Baniso -3
1-5.6905 Å20 Å20 Å2
2---1.6664 Å20 Å2
3----4.0241 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→18.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 31 269 3077
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012885HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.123904HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d21.91020SINUSOIDAL2
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2774 135 5.33 %
Rwork0.2586 2397 -
all0.2596 2532 -
obs-2532 98.23 %
Refinement TLS params.Method: refined / Origin x: 24.0974 Å / Origin y: 44.0243 Å / Origin z: 9.5988 Å
111213212223313233
T0.082 Å2-0.0101 Å2-0.0012 Å2--0.0318 Å2-0.0029 Å2---0.0741 Å2
L0.5541 °2-0.0469 °20.0557 °2-0.1012 °20.0228 °2--0.4298 °2
S0.0009 Å °-0.0465 Å °0.0514 Å °-0.0133 Å °-0.0056 Å °-0.0194 Å °-0.0443 Å °0.019 Å °0.0047 Å °

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