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- PDB-6l24: Crystal structure of CK2a1 H115Y/V116I with hematein -

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Basic information

Entry
Database: PDB / ID: 6l24
TitleCrystal structure of CK2a1 H115Y/V116I with hematein
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / protein kinase / 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 / 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 / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / 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 / 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-E3U / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40009490218 Å
AuthorsTsuyuguchi, M. / Kinoshita, T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Structural insights for producing CK2 alpha 1-specific inhibitors.
Authors: Tsuyuguchi, M. / Nakaniwa, T. / Hirasawa, A. / Nakanishi, I. / Kinoshita, T.
History
DepositionOct 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)40,8182
Polymers40,5171
Non-polymers3001
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16450 Å2
Unit cell
Length a, b, c (Å)51.588, 78.823, 79.964
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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 II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 40517.246 Da / Num. of mol.: 1 / Mutation: H115Y, V116I
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-E3U / (6aR)-3,4,6a,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2,1-c]chromen-9-one


Mass: 300.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Ethylene glycol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→43.35 Å / Num. obs: 13323 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.2656223859 Å2 / Rmerge(I) obs: 0.193 / Net I/σ(I): 8
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.845 / Num. unique obs: 1373

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAR

3war


Resolution: 2.40009490218→43.3496377373 Å / SU ML: 0.311002460556 / Cross valid method: FREE R-VALUE / σ(F): 1.33789305055 / Phase error: 26.3102444413
RfactorNum. reflection% reflection
Rfree0.262989158332 1332 10.0323868344 %
Rwork0.183598204414 --
obs0.191778227782 13277 99.9322595213 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.5201596931 Å2
Refinement stepCycle: LAST / Resolution: 2.40009490218→43.3496377373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 0 22 85 2927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008175652063082945
X-RAY DIFFRACTIONf_angle_d1.242101379823994
X-RAY DIFFRACTIONf_chiral_restr0.0450088330164407
X-RAY DIFFRACTIONf_plane_restr0.00494031577816507
X-RAY DIFFRACTIONf_dihedral_angle_d16.66982603581106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.48590.3709778839961280.2295734469031172X-RAY DIFFRACTION99.846390169
2.4859-2.58540.2729681404361330.2017014211061171X-RAY DIFFRACTION100
2.5854-2.7030.3300454828011330.2097106822291169X-RAY DIFFRACTION99.9232540292
2.703-2.84550.2543978492891290.1840282842841169X-RAY DIFFRACTION100
2.8455-3.02380.3029225504421320.1934815977261187X-RAY DIFFRACTION100
3.0238-3.25720.285538581441310.1950472272291185X-RAY DIFFRACTION100
3.2572-3.58480.2764759171281300.1786008310781178X-RAY DIFFRACTION99.923605806
3.5848-4.10320.2446559866331350.1701051721211214X-RAY DIFFRACTION100
4.1032-5.16820.2128993768531380.1545300736771214X-RAY DIFFRACTION100
5.1682-43.340.2436449520271430.191851379291286X-RAY DIFFRACTION99.7208653175

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