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- PDB-9epw: Crystal structure of human Casein Kinase II subunit alpha (CK2a1)... -

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Basic information

Entry
Database: PDB / ID: 9epw
TitleCrystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric ligand FGC3336
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2 / Kinase / Chemical / allosteric Inhibitor
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 / Maturation of hRSV A proteins / Sin3-type complex ...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 / Maturation of hRSV A proteins / Sin3-type complex / 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 / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / DNA damage response / 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
: / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKraemer, A. / Greco, F. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
Citation
Journal: Eur.J.Med.Chem. / Year: 2024
Title: Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting.
Authors: Greco, F.A. / Kramer, A. / Wahl, L. / Elson, L. / Ehret, T.A.L. / Gerninghaus, J. / Mockel, J. / Muller, S. / Hanke, T. / Knapp, S.
#1: Journal: Biorxiv / Year: 2024
Title: Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting
Authors: Greco, F.A. / Kramer, A. / Wahl, L. / Elson, L. / Ehret, T.A.L. / Gerninghaus, J. / Mockel, J. / Muller, S. / Hanke, T. / Knapp, S.
History
DepositionMar 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3427
Polymers40,3281
Non-polymers1,0146
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-64 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.063, 72.063, 133.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 40327.977 Da / Num. of mol.: 1
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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1H6F / ~{N}-[(3-chloranyl-4-phenyl-phenyl)methyl]-2-[1-(3-methylquinolin-8-yl)sulfonylpiperidin-4-yl]ethanamine / SCH66336


Mass: 534.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H32ClN3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.3→48.98 Å / Num. obs: 16320 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.991 / Net I/σ(I): 5.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1541 / CC1/2: 0.742

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.98 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.881 / SU B: 25.676 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.48 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30791 809 5 %RANDOM
Rwork0.25888 ---
obs0.26137 15454 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.536 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å20 Å2
2--0.99 Å2-0 Å2
3----1.99 Å2
Refinement stepCycle: 1 / Resolution: 2.3→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 62 33 2779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122803
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162505
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.6673816
X-RAY DIFFRACTIONr_angle_other_deg0.5421.6095738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.288518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25710438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02672
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9383.0631310
X-RAY DIFFRACTIONr_mcbond_other1.933.0621310
X-RAY DIFFRACTIONr_mcangle_it3.125.5081634
X-RAY DIFFRACTIONr_mcangle_other3.1215.5091635
X-RAY DIFFRACTIONr_scbond_it2.2263.1821493
X-RAY DIFFRACTIONr_scbond_other1.8633.131482
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9975.7152165
X-RAY DIFFRACTIONr_long_range_B_refined5.56140.15750
X-RAY DIFFRACTIONr_long_range_B_other5.56140.15751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 41 -
Rwork0.337 1115 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -13.57 Å / Origin y: 9.4871 Å / Origin z: 8.6988 Å
111213212223313233
T0.0249 Å2-0.0034 Å20.0559 Å2-0.0686 Å20.0251 Å2--0.1883 Å2
L1.49 °2-0.0597 °20.042 °2-2.2062 °20.6937 °2--1.7919 °2
S0.0826 Å °-0.228 Å °0.0948 Å °0.1661 Å °0.0067 Å °0.2088 Å °0.0149 Å °-0.2303 Å °-0.0893 Å °

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