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- PDB-6yum: CK2 alpha bound to unclosed Macrocycle -

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Basic information

Entry
Database: PDB / ID: 6yum
TitleCK2 alpha bound to unclosed Macrocycle
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / Kinase / Macrocycle / Inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Sin3-type complex / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway ...regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Sin3-type complex / Receptor Mediated Mitophagy / 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 / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Hsp90 protein binding / 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 / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / 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 / nucleus / identical protein binding / 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-PQ8 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKraemer, A. / Hanke, T. / Kurz, C. / Celik, I. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Optimization of pyrazolo[1,5-a]pyrimidines lead to the identification of a highly selective casein kinase 2 inhibitor.
Authors: Kramer, A. / Kurz, C.G. / Berger, B.T. / Celik, I.E. / Tjaden, A. / Greco, F.A. / Knapp, S. / Hanke, T.
History
DepositionApr 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Casein kinase II subunit alpha
GGG: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,91010
Polymers90,4172
Non-polymers1,4938
Water362
1
AAA: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9555
Polymers45,2091
Non-polymers7474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
GGG: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9555
Polymers45,2091
Non-polymers7474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.479, 125.479, 124.655
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A G)

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Components

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


Mass: 45208.559 Da / Num. of mol.: 2
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PQ8 / 4-[5-[2-(2-hydroxyethyloxy)ethyl-[(2-methylpropan-2-yl)oxycarbonyl]amino]pyrazolo[1,5-a]pyrimidin-3-yl]-2-oxidanyl-benzoic acid


Mass: 458.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26N4O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5 0.2 ammonia sulphate 30% PEG 5000 MME 10 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000031 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.75→44.36 Å / Num. obs: 26481 / % possible obs: 99.9 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rpim(I) all: 0.045 / Net I/σ(I): 10.5
Reflection shellResolution: 2.75→2.9 Å / Num. unique obs: 3806 / CC1/2: 0.923 / Rpim(I) all: 0.316 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE2
Resolution: 2.75→44.36 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.771 / SU ML: 0.397 / Cross valid method: FREE R-VALUE / ESU R: 0.938 / ESU R Free: 0.37
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2838 1407 5.324 %
Rwork0.2626 --
all0.264 --
obs-26427 99.789 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.329 Å2
Baniso -1Baniso -2Baniso -3
1--0.185 Å20 Å20 Å2
2---0.185 Å20 Å2
3---0.371 Å2
Refinement stepCycle: LAST / Resolution: 2.75→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 96 2 5421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135563
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174897
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0440.018429
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.6467567
X-RAY DIFFRACTIONr_angle_other_deg1.51.59311259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.05521.362323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24615872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4931542
X-RAY DIFFRACTIONr_chiral_restr0.0820.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021279
X-RAY DIFFRACTIONr_nbd_refined0.2190.21090
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.24642
X-RAY DIFFRACTIONr_nbtor_refined0.180.22719
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.283
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1120.213
X-RAY DIFFRACTIONr_nbd_other0.2110.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.26
X-RAY DIFFRACTIONr_mcbond_it2.2347.542625
X-RAY DIFFRACTIONr_mcbond_other2.2327.5352620
X-RAY DIFFRACTIONr_mcangle_it3.78311.3033273
X-RAY DIFFRACTIONr_mcangle_other3.78311.3043272
X-RAY DIFFRACTIONr_scbond_it1.9357.6842938
X-RAY DIFFRACTIONr_scbond_other1.9347.6842938
X-RAY DIFFRACTIONr_scangle_it3.38711.4834294
X-RAY DIFFRACTIONr_scangle_other3.38611.4834295
X-RAY DIFFRACTIONr_lrange_it7.686141.49322709
X-RAY DIFFRACTIONr_lrange_other7.686141.49322710
X-RAY DIFFRACTIONr_ncsr_local_group_10.0960.0510384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.8210.4431250.4261784X-RAY DIFFRACTION99.8953
2.821-2.8990.353970.4021792X-RAY DIFFRACTION99.8942
2.899-2.9830.413890.3611725X-RAY DIFFRACTION99.9449
2.983-3.0740.326930.3391670X-RAY DIFFRACTION100
3.074-3.1750.347980.3361610X-RAY DIFFRACTION99.7664
3.175-3.2860.333910.2891597X-RAY DIFFRACTION100
3.286-3.410.307800.2681516X-RAY DIFFRACTION99.9374
3.41-3.5490.2921020.2661462X-RAY DIFFRACTION99.8723
3.549-3.7070.282660.2531388X-RAY DIFFRACTION98.5763
3.707-3.8870.247650.241365X-RAY DIFFRACTION99.7211
3.887-4.0970.239590.2281307X-RAY DIFFRACTION99.9268
4.097-4.3450.256550.2311238X-RAY DIFFRACTION100
4.345-4.6440.285610.2091173X-RAY DIFFRACTION100
4.644-5.0150.248660.1991083X-RAY DIFFRACTION100
5.015-5.4920.318570.243992X-RAY DIFFRACTION99.9048
5.492-6.1370.295420.255921X-RAY DIFFRACTION100
6.137-7.0810.342520.262819X-RAY DIFFRACTION99.7709
7.081-8.6590.226520.23676X-RAY DIFFRACTION99.4536
8.659-12.1880.209370.23562X-RAY DIFFRACTION99.8333

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