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- PDB-7a1b: Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene... -

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Basic information

Entry
Database: PDB / ID: 7a1b
TitleCrystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 5,6-dibromo-1H-triazolo[4,5-b]pyridine
ComponentsCasein kinase II subunit alpha'Casein kinase 2
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / ATP-competitive inhibitor
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / 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 mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / 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 / negative regulation of ubiquitin-dependent protein catabolic process / acrosomal vesicle / Signal transduction by L1 / liver regeneration / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / spermatogenesis / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin / nucleoplasm / ATP binding / nucleus / 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
5,6-dibromo-1H-triazolo[4,5-b]pyridine / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.287 Å
AuthorsNiefind, K. / Lindenblatt, D. / Toelzer, C. / Bretner, M. / Chojnacki, K. / Wielechowska, M. / Winska, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/4-2 Germany
Citation
Journal: Bioorg.Chem. / Year: 2021
Title: Synthesis, biological properties and structural study of new halogenated azolo[4,5-b]pyridines as inhibitors of CK2 kinase.
Authors: Chojnacki, K. / Lindenblatt, D. / Winska, P. / Wielechowska, M. / Toelzer, C. / Niefind, K. / Bretner, M.
#1: Journal: Bioorg. Chem. / Year: 2018
Title: Biological properties and structural study of new aminoalkyl derivatives of benzimidazole and benzotriazole, dual inhibitors of CK2 and PIM1 kinases.
Authors: Chojnacki, K. / Winska, P. / Wielechowska, M. / Lukowska-Chojnacka, E. / Toelzer, C. / Niefind, K. / Bretner, M.
#2: Journal: ACS Omega / Year: 2019
Title: Diacritic Binding of an Indenoindole Inhibitor by CK2alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2alpha' Structures.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Hochscherf, J. / Witulski, B. / Bouaziz, Z. / Marminon, C. / Bretner, M. / Le Borgne, M. / Jose, J. / Niefind, K.
#3: Journal: J. Med. Chem. / Year: 2020
Title: Structural and Mechanistic Basis of the Inhibitory Potency of Selected 2-Aminothiazole Compounds on Protein Kinase CK2.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Jose, J. / Niefind, K.
History
DepositionAug 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)43,62411
Polymers42,8801
Non-polymers74410
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-11 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.256, 47.593, 50.550
Angle α, β, γ (deg.)113.229, 89.996, 91.127
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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: 42879.867 Da / Num. of mol.: 1 / Mutation: C336S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P19784, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 301 molecules

#2: Chemical ChemComp-QXW / 5,6-dibromo-1H-triazolo[4,5-b]pyridine / 5,6-bis(bromanyl)-1~{H}-[1,2,3]triazolo[4,5-b]pyridine


Mass: 277.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H2Br2N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser) ...Details: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the inhibitor 5,6-dibromo-1H-triazolo[4,5-b]pyridine by extensive crystal soaking.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.287→46.45 Å / Num. obs: 70878 / % possible obs: 70.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.05 / Rrim(I) all: 0.093 / Rsym value: 0.078 / Net I/σ(I): 8.3
Reflection shellResolution: 1.287→1.412 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3544 / CC1/2: 0.519 / Rpim(I) all: 0.512 / Rrim(I) all: 0.977 / Rsym value: 0.829 / % possible all: 14.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.287→46.45 Å / SU ML: 0.142 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.0485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1925 1411 1.99 %
Rwork0.1573 69448 -
obs0.158 70859 69.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.92 Å2
Refinement stepCycle: LAST / Resolution: 1.287→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 38 291 3088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713033
X-RAY DIFFRACTIONf_angle_d0.8914106
X-RAY DIFFRACTIONf_chiral_restr0.0751416
X-RAY DIFFRACTIONf_plane_restr0.0057535
X-RAY DIFFRACTIONf_dihedral_angle_d18.5611168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.330.2834130.2099411X-RAY DIFFRACTION4.17
1.33-1.380.2949250.22231479X-RAY DIFFRACTION14.8
1.38-1.440.2405660.22023654X-RAY DIFFRACTION36.23
1.44-1.520.25111550.21146795X-RAY DIFFRACTION68.49
1.52-1.610.25951770.19219131X-RAY DIFFRACTION91.06
1.61-1.740.23591960.16869596X-RAY DIFFRACTION95.65
1.74-1.910.18641890.15079605X-RAY DIFFRACTION95.73
1.91-2.190.18131890.13159622X-RAY DIFFRACTION96.31
2.19-2.760.17862010.14439574X-RAY DIFFRACTION95.66
2.76-46.450.17772000.15999581X-RAY DIFFRACTION95.7

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