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- PDB-7zwg: The Crystal structure of RO4493940 bound to CK2alpha -

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Basic information

Entry
Database: PDB / ID: 7zwg
TitleThe Crystal structure of RO4493940 bound to CK2alpha
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Selective kinase inhibitors
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 / 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 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 / 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 / negative regulation of translation / 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 / 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
ACETATE ION / Chem-R7W / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.31 Å
AuthorsBrear, P. / Hyvonen, M.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors.
Authors: Reinecke, M. / Brear, P. / Vornholz, L. / Berger, B.T. / Seefried, F. / Wilhelm, S. / Samaras, P. / Gyenis, L. / Litchfield, D.W. / Medard, G. / Muller, S. / Ruland, J. / Hyvonen, M. / Wilhelm, M. / Kuster, B.
History
DepositionMay 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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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)39,6085
Polymers39,0311
Non-polymers5774
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-7 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.514, 45.289, 62.979
Angle α, β, γ (deg.)90.000, 111.540, 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 / CK II alpha


Mass: 39031.391 Da / Num. of mol.: 1 / Mutation: K74A, K75A, K76A, R21S
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

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Non-polymers , 5 types, 240 molecules

#2: Chemical ChemComp-R7W / (5~{Z})-5-(quinolin-6-ylmethylidene)-1,3-thiazolidine-2,4-dione


Mass: 256.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H8N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 38.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 112.5mM Mes, 35% glycerol ethoxylate, 180 mM ammonium acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.31→50.08 Å / Num. obs: 73264 / % possible obs: 98.3 % / Redundancy: 18.9 % / CC1/2: 1 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.031 / Rrim(I) all: 0.137 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.31-1.3818.23.574188745103880.5680.8463.675195.9
4.13-50.0818.10.03944659246410.0090.0465.899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVH

5cvh


Resolution: 1.31→50.08 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 3622 4.96 %RANDOM
Rwork0.1881 69460 --
obs0.1888 73082 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.12 Å2 / Biso mean: 24.7142 Å2 / Biso min: 11.47 Å2
Refinement stepCycle: final / Resolution: 1.31→50.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 38 236 3023
Biso mean--25.87 29.25 -
Num. residues----327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.31-1.32250.29161230.3084251191
1.3225-1.34060.30321470.2916255794
1.3406-1.35980.31771280.2767259096
1.3598-1.38010.31571380.2744259696
1.3801-1.40160.28221570.2598262196
1.4016-1.42460.26631360.2539264597
1.4246-1.44920.24971290.2415260197
1.4492-1.47550.2381280.2315266097
1.4755-1.50390.23921360.2223266097
1.5039-1.53460.21881400.2226265098
1.5346-1.5680.21781320.2136266598
1.568-1.60450.24521630.2094261698
1.6045-1.64460.2261450.2062268898
1.6446-1.6890.21191620.2011263598
1.689-1.73880.20061410.1969268598
1.7388-1.79490.23861130.1985270199
1.7949-1.8590.2311330.1957271499
1.859-1.93350.2231320.1928269699
1.9335-2.02150.18561200.1894272399
2.0215-2.1280.18821560.1795268699
2.128-2.26140.19191250.1817275899
2.2614-2.4360.19651390.18282722100
2.436-2.68110.21311290.18892766100
2.6811-3.0690.19891800.19382701100
3.069-3.86640.17871290.16742790100
3.8664-50.080.17931610.16112823100

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