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- PDB-6l1z: Crystal structure of CK2a1 with hematein -

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Basic information

Entry
Database: PDB / ID: 6l1z
TitleCrystal structure of CK2a1 with hematein
ComponentsCasein Kinase 2 subunit alpha
KeywordsTRANSFERASE / protein kinase / inhibitor / complex
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / 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 proteasomal ubiquitin-dependent protein catabolic 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 / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / 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-E3U / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.90820949507 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 2 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7782
Polymers40,4781
Non-polymers3001
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15590 Å2
Unit cell
Length a, b, c (Å)51.609, 78.664, 79.903
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 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-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.: 149 / 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 Å3/Da / Density % sol: 38.61 %
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: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.908→50 Å / Num. obs: 25447 / % possible obs: 97.9 % / Redundancy: 7 % / Biso Wilson estimate: 24.5346573878 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 27.8
Reflection shellResolution: 1.91→1.94 Å / Rmerge(I) obs: 0.415 / Num. unique obs: 1038

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Processing

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

3war


Resolution: 1.90820949507→24.6304252789 Å / SU ML: 0.152616649392 / Cross valid method: FREE R-VALUE / σ(F): 1.34161676892 / Phase error: 20.3567156158
RfactorNum. reflection% reflection
Rfree0.21629499244 1302 5.12699350266 %
Rwork0.194197591942 24093 -
obs0.195268050958 25395 97.8348807643 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.6611674599 Å2
Refinement stepCycle: LAST / Resolution: 1.90820949507→24.6304252789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 22 149 2950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004400344224162879
X-RAY DIFFRACTIONf_angle_d1.545607441523900
X-RAY DIFFRACTIONf_chiral_restr0.103321492099402
X-RAY DIFFRACTIONf_plane_restr0.00641990705241498
X-RAY DIFFRACTIONf_dihedral_angle_d13.39270695211083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.90821-1.98460.2544911179821060.2199174730172314X-RAY DIFFRACTION85.5425945564
1.9846-2.07490.2011107393381520.2007364846232576X-RAY DIFFRACTION95.9549771368
2.0749-2.18420.2114204495231310.1854961110332679X-RAY DIFFRACTION99.539496989
2.1842-2.32090.2315621129481440.1896086898752705X-RAY DIFFRACTION99.7549019608
2.3209-2.50.2406854270841580.195053704552701X-RAY DIFFRACTION99.7905759162
2.5-2.75130.2023048257331600.1996553567582700X-RAY DIFFRACTION99.8952148096
2.7513-3.14870.2139364162911510.1933445471112736X-RAY DIFFRACTION99.9653739612
3.1487-3.96430.1937764831251560.1844402314742790X-RAY DIFFRACTION100
3.9643-24.630.2322041275371440.1987044011212892X-RAY DIFFRACTION99.7699638515

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