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- PDB-7l1x: Structure of human CK2 alpha kinase (catalytic subunit) with the ... -

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Basic information

Entry
Database: PDB / ID: 7l1x
TitleStructure of human CK2 alpha kinase (catalytic subunit) with the inhibitor 108600.
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / inhibitor 108600 / TRANSFERASE / 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 / 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-ON6 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRechkoblit, O. / Aggarwal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)BC161776 United States
CitationJournal: Nat Commun / Year: 2021
Title: Simultaneous CK2/TNIK/DYRK1 inhibition by 108600 suppresses triple negative breast cancer stem cells and chemotherapy-resistant disease.
Authors: Sato, K. / Padgaonkar, A.A. / Baker, S.J. / Cosenza, S.C. / Rechkoblit, O. / Subbaiah, D.R.C.V. / Domingo-Domenech, J. / Bartkowski, A. / Port, E.R. / Aggarwal, A.K. / Ramana Reddy, M.V. / ...Authors: Sato, K. / Padgaonkar, A.A. / Baker, S.J. / Cosenza, S.C. / Rechkoblit, O. / Subbaiah, D.R.C.V. / Domingo-Domenech, J. / Bartkowski, A. / Port, E.R. / Aggarwal, A.K. / Ramana Reddy, M.V. / Irie, H.Y. / Premkumar Reddy, E.
History
DepositionDec 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9507
Polymers39,9361
Non-polymers1,0156
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.348, 45.981, 63.683
Angle α, β, γ (deg.)90.000, 111.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39935.547 Da / Num. of mol.: 1 / Fragment: Catalytic subunit
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ON6 / (2~{Z})-6-[[2,6-bis(chloranyl)phenyl]methylsulfonyl]-2-[[4-oxidanyl-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]methylidene]-4~{H}-1,4-benzothiazin-3-one


Mass: 538.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H15Cl2N2O6S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris-HCl pH 7.5 200 mM ammonium sulfate 21% PEG5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98011 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 28233 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 18.51
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.5 / Num. unique obs: 1485

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OWJ

3owj


Resolution: 1.8→24.88 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.564 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1418 5 %RANDOM
Rwork0.1728 ---
obs0.1754 26802 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.42 Å2 / Biso mean: 34.827 Å2 / Biso min: 19.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å2-0 Å2-0.35 Å2
2--1.27 Å20 Å2
3---0.55 Å2
Refinement stepCycle: final / Resolution: 1.8→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 71 221 3038
Biso mean--52.73 41.71 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122889
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172732
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.6533921
X-RAY DIFFRACTIONr_angle_other_deg0.4351.5846188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28121.13177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54715492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2351525
X-RAY DIFFRACTIONr_chiral_restr0.0650.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023223
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02746
LS refinement shellResolution: 1.804→1.851 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 67 -
Rwork0.262 1536 -
all-1603 -
obs--74.59 %

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