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- PDB-7zy2: Crystal structure of compound 7 bound to CK2alpha -

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Basic information

Entry
Database: PDB / ID: 7zy2
TitleCrystal structure of compound 7 bound to CK2alpha
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Fragment based drug discovery
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 / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...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 / Sin3-type complex / 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 proteasomal ubiquitin-dependent protein catabolic process / : / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / rhythmic process / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / regulation of cell cycle / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / 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 / ADENOSINE-5'-TRIPHOSPHATE / 5-bromanyl-1~{H}-indole / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsBrear, P. / Fusco, C. / Atkinson, E. / Rossmann, M. / Francis, N. / Iegre, J. / Hyvonen, M. / Spring, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust107714/Z/15/Z United Kingdom
Wellcome Trust090340/Z/09/Z United Kingdom
CitationJournal: Rsc Med Chem / Year: 2022
Title: A fragment-based approach leading to the discovery of inhibitors of CK2 alpha with a novel mechanism of action.
Authors: Brear, P. / De Fusco, C. / Atkinson, E.L. / Iegre, J. / Francis-Newton, N.J. / Venkitaraman, A.R. / Hyvonen, M. / Spring, D.R.
History
DepositionMay 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)40,0496
Polymers39,0311
Non-polymers1,0175
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-4 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.782, 45.916, 63.286
Angle α, β, γ (deg.)90.000, 111.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39031.391 Da / Num. of mol.: 1 / Mutation: R21S, K74A, K75A, K76A
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-H4N / 5-bromanyl-1~{H}-indole


Mass: 196.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6BrN / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.507→54.55 Å / Num. obs: 48182 / % possible obs: 96.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 20.38 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Rsym value: 0.061 / Net I/σ(I): 15.4 / Num. measured all: 243427 / Scaling rejects: 37
Reflection shellResolution: 1.507→1.512 Å / Redundancy: 5 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 2.1 / Num. measured all: 35602 / Num. unique obs: 6913 / CC1/2: 0.781 / Rpim(I) all: 0.325 / Rrim(I) all: 0.748 / Rsym value: 0.719 / Net I/σ(I) obs: 2.4 / % possible all: 94.3

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MOH

5moh


Resolution: 1.51→22.11 Å / Cor.coef. Fo:Fc: 0.9552 / Cor.coef. Fo:Fc free: 0.9473 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.082 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 2415 5.04 %RANDOM
Rwork0.1878 ---
obs0.189 47870 96.94 %-
Displacement parametersBiso max: 109.52 Å2 / Biso mean: 24.86 Å2 / Biso min: 7.77 Å2
Baniso -1Baniso -2Baniso -3
1--2.476 Å20 Å20.2841 Å2
2--2.9375 Å20 Å2
3----0.4615 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: final / Resolution: 1.51→22.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 59 241 3048
Biso mean--29.33 30.49 -
Num. residues----327
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1052SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes483HARMONIC5
X-RAY DIFFRACTIONt_it2993HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion359SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3680SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2993HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4073HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion15.74
LS refinement shellResolution: 1.51→1.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3162 172 4.97 %
Rwork0.2927 3292 -
all0.2938 3464 -
obs--96.94 %

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