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- PDB-6yul: CK2 alpha bound to Macrocycle -

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Basic information

Entry
Database: PDB / ID: 6yul
TitleCK2 alpha bound to 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 / 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 / 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 / Hsp90 protein binding / peptidyl-threonine phosphorylation / 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 / rhythmic process / double-strand break repair / KEAP1-NFE2L2 pathway / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / 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
Chem-PQ5 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)92,05814
Polymers90,4172
Non-polymers1,64112
Water79344
1
AAA: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0297
Polymers45,2091
Non-polymers8216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
GGG: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0297
Polymers45,2091
Non-polymers8216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.649, 128.649, 125.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PQ5 / 7,10-Dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.12,6.017,20]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxylic acid


Mass: 340.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonia sulphate, 0.1 MES pH 6.5, 31-35% (v/v) polyethylene glycol 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: 0.999998 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: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.4→45.48 Å / Num. obs: 41786 / % possible obs: 100 % / Redundancy: 14.9 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 16.9
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 4317 / CC1/2: 0.718 / Rpim(I) all: 0.426

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE2

3pe2


Resolution: 2.4→45.48 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.6 / SU ML: 0.173 / Cross valid method: FREE R-VALUE / ESU R: 0.301 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2324 2065 4.949 %
Rwork0.2168 --
all0.218 --
obs-41726 99.976 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.533 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.421 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 100 44 5594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135692
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175091
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0480.018451
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.6467727
X-RAY DIFFRACTIONr_angle_other_deg1.5121.58911731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7321.183338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88815941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2481547
X-RAY DIFFRACTIONr_chiral_restr0.0940.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021301
X-RAY DIFFRACTIONr_nbd_refined0.2190.21054
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.24679
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22752
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22821
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.27
X-RAY DIFFRACTIONr_nbd_other0.1650.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.25
X-RAY DIFFRACTIONr_mcbond_it3.1086.092648
X-RAY DIFFRACTIONr_mcbond_other3.1076.0892646
X-RAY DIFFRACTIONr_mcangle_it4.9939.1263304
X-RAY DIFFRACTIONr_mcangle_other4.9939.1283305
X-RAY DIFFRACTIONr_scbond_it3.2976.2963044
X-RAY DIFFRACTIONr_scbond_other3.2756.2753025
X-RAY DIFFRACTIONr_scangle_it5.2829.3464423
X-RAY DIFFRACTIONr_scangle_other5.269.3154394
X-RAY DIFFRACTIONr_lrange_it8.078120.86211823
X-RAY DIFFRACTIONr_lrange_other8.078120.85711824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.3051430.32895X-RAY DIFFRACTION100
2.462-2.530.3321740.2882780X-RAY DIFFRACTION100
2.53-2.6030.3381040.2772768X-RAY DIFFRACTION100
2.603-2.6830.3191100.262696X-RAY DIFFRACTION100
2.683-2.7710.2911440.2492559X-RAY DIFFRACTION100
2.771-2.8680.3061200.2472514X-RAY DIFFRACTION100
2.868-2.9760.2541530.2262389X-RAY DIFFRACTION100
2.976-3.0980.281260.2272330X-RAY DIFFRACTION100
3.098-3.2350.239840.2282278X-RAY DIFFRACTION100
3.235-3.3930.2431030.2182148X-RAY DIFFRACTION100
3.393-3.5760.2271330.2282029X-RAY DIFFRACTION99.9538
3.576-3.7930.2561070.2181927X-RAY DIFFRACTION100
3.793-4.0540.2141220.1991798X-RAY DIFFRACTION100
4.054-4.3780.195980.1821700X-RAY DIFFRACTION100
4.378-4.7950.195590.1621615X-RAY DIFFRACTION100
4.795-5.3590.197770.1771443X-RAY DIFFRACTION100
5.359-6.1850.224770.2171273X-RAY DIFFRACTION100
6.185-7.5660.286460.2361122X-RAY DIFFRACTION100
7.566-10.6630.186560.194872X-RAY DIFFRACTION100

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