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- PDB-6l22: Crystal structure of CK2a1 H115Y with hematein -

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Basic information

Entry
Database: PDB / ID: 6l22
TitleCrystal structure of CK2a1 H115Y with hematein
ComponentsCasein kinase II subunit alpha
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 / Synthesis of PC / Sin3-type complex / 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 / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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: 2.12318084151 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

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8032
Polymers40,5031
Non-polymers3001
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16080 Å2
Unit cell
Length a, b, c (Å)48.107, 79.21, 82.657
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 / CK II alpha


Mass: 40503.219 Da / Num. of mol.: 1 / Mutation: H115Y
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


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.95 Å3/Da / Density % sol: 36.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 25% 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: 2.12→50 Å / Num. obs: 18488 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 20.6256896581 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 10
Reflection shellResolution: 2.12→2.16 Å / Rmerge(I) obs: 0.459 / Num. unique obs: 885

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAR

3war


Resolution: 2.12318084151→41.3285 Å / SU ML: 0.220094981737 / Cross valid method: FREE R-VALUE / σ(F): 1.37279545709 / Phase error: 22.4888922019
RfactorNum. reflection% reflection
Rfree0.242924126409 1845 10.0375387629 %
Rwork0.180247346967 16536 -
obs0.18660976503 18381 99.5720476706 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.5842533527 Å2
Refinement stepCycle: LAST / Resolution: 2.12318084151→41.3285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2819 0 22 158 2999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007984213589172953
X-RAY DIFFRACTIONf_angle_d1.122296687344007
X-RAY DIFFRACTIONf_chiral_restr0.0459823010572408
X-RAY DIFFRACTIONf_plane_restr0.0056911082545509
X-RAY DIFFRACTIONf_dihedral_angle_d14.59328097371109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1232-2.18060.2680135750331250.2012476477161232X-RAY DIFFRACTION96.3094393187
2.1806-2.24470.2776107809861490.1794370135631210X-RAY DIFFRACTION99.4147768837
2.2447-2.31720.2391832446111420.1816157149821248X-RAY DIFFRACTION99.8563218391
2.3172-2.40.2628394828981390.1683072183051279X-RAY DIFFRACTION100
2.4-2.49610.251135477291410.1670473546821254X-RAY DIFFRACTION100
2.4961-2.60970.202290073621390.1688679345451240X-RAY DIFFRACTION100
2.6097-2.74720.2680848858171390.1821705411481283X-RAY DIFFRACTION100
2.7472-2.91930.2538467361471390.1768474153691264X-RAY DIFFRACTION100
2.9193-3.14460.2433066732821470.1825120904851260X-RAY DIFFRACTION100
3.1446-3.4610.2507759677621430.1679645127671304X-RAY DIFFRACTION100
3.461-3.96140.2226191886431470.1708542446951282X-RAY DIFFRACTION100
3.9614-4.98960.2076628423711420.1643166025911313X-RAY DIFFRACTION100
4.9896-41.320.2724184704071530.2279962048091367X-RAY DIFFRACTION98.9583333333

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