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- PDB-5osl: The crystal structure of CK2alpha in complex with compound 7 -

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Basic information

Entry
Database: PDB / ID: 5osl
TitleThe crystal structure of CK2alpha in complex with compound 7
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / CK2alpha / CK2a / fragment based drug discovery / high concentration screening / selective ATP competitive inhibitors / surface entrophy reduction
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 / Maturation of hRSV A proteins / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC ...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 / Maturation of hRSV A proteins / 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 / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / 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 / negative regulation of translation / protein stabilization / non-specific serine/threonine protein kinase / regulation of cell cycle / 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
2-[4-(aminomethyl)-2-chloranyl-phenyl]phenol / ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBrear, P. / De Fusco, C. / Iegre, J. / Yoshida, M. / Mitchell, S. / Rossmann, M. / Carro, L. / Sore, H. / Hyvonen, M. / Spring, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust090340/Z/09/Z United Kingdom
Wellcome Trust107714/Z/15/Z United Kingdom
CitationJournal: Chem Sci / Year: 2018
Title: Second-generation CK2 alpha inhibitors targeting the alpha D pocket.
Authors: Iegre, J. / Brear, P. / De Fusco, C. / Yoshida, M. / Mitchell, S.L. / Rossmann, M. / Carro, L. / Sore, H.F. / Hyvonen, M. / Spring, D.R.
History
DepositionAug 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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)41,9439
Polymers40,7861
Non-polymers1,1568
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-37 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.609, 46.395, 62.761
Angle α, β, γ (deg.)90.000, 112.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 40786.402 Da / Num. of mol.: 1 / Fragment: residues 2-329 / Mutation: R21S, K74A, K75A, K76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 242 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-A9K / 2-[4-(aminomethyl)-2-chloranyl-phenyl]phenol


Mass: 233.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12ClNO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1.94 Å3/Da / Density % sol: 36.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→36.27 Å / Num. obs: 23058 / % possible obs: 99.5 % / Redundancy: 14.12 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 17.63 / Num. measured all: 327090
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
1.95-1.985.370.58221013190.9
1.98-2.017.030.5499901100
2.01-2.057.620.49511941100
2.05-2.18.520.44313801100
2.1-2.149.780.4069811100
2.14-2.1910.330.3811731100
2.19-2.2511.370.36412601100
2.25-2.3112.890.30911201100
2.31-2.3814.020.28611771100
2.38-2.4615.210.25811991100
2.46-2.5515.570.23311591100
2.55-2.6515.990.21211241100
2.65-2.7716.360.17811431100
2.77-2.9216.890.15411761100
2.92-3.1117.450.12411981100
3.11-3.3518.640.10211181100
3.35-3.719.650.0811881100
3.7-4.2519.970.05911601100
4.25-5.3920.030.05111501100
5.39-8.1619.620.064809199.6
8.16-36.2717.970.055346198.9

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Processing

Software
NameVersionClassification
XPREP2013/3data scaling
BUSTER2.10.1refinement
PDB_EXTRACT3.23data extraction
XPREPdata reduction
PHASERphasing
XPREPdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVH

5cvh


Resolution: 1.95→36.27 Å / Cor.coef. Fo:Fc: 0.9506 / Cor.coef. Fo:Fc free: 0.9177 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.179 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1157 5.03 %RANDOM
Rwork0.1629 ---
obs0.1653 23007 99.93 %-
Displacement parametersBiso max: 101.07 Å2 / Biso mean: 20.45 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.4666 Å20 Å2-0.2856 Å2
2---0.3458 Å20 Å2
3---0.8123 Å2
Refine analyzeLuzzati coordinate error obs: 0.184 Å
Refinement stepCycle: final / Resolution: 1.95→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 90 234 3078
Biso mean--23.84 26.72 -
Num. residues----328
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1035SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes489HARMONIC5
X-RAY DIFFRACTIONt_it2972HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion355SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3592SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2972HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4038HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion16.52
LS refinement shellResolution: 1.95→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2591 120 4.34 %
Rwork0.1996 2645 -
all0.2019 2765 -
obs--99.93 %

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