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- PDB-7zyk: Compound 9 Bound to CK2alpha -

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Basic information

Entry
Database: PDB / ID: 7zyk
TitleCompound 9 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 / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...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 / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / 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 / Regulation of PTEN stability and activity / Wnt signaling pathway / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / 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 / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / 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
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Chem-KEC / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsBrear, P. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust 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 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)39,9647
Polymers39,0311
Non-polymers9336
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.343, 45.842, 63.266
Angle α, β, γ (deg.)90.000, 111.380, 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-KEC / 2-(5-bromanyl-6-chloranyl-1~{H}-indol-3-yl)ethanenitrile


Mass: 269.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6BrClN2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.305→54.33 Å / Num. obs: 65260 / % possible obs: 86.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 16.27 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Rsym value: 0.063 / Net I/σ(I): 15.1
Reflection shellResolution: 1.305→1.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.6 / Num. measured all: 992 / Num. unique obs: 277 / CC1/2: 0.648 / Rpim(I) all: 0.381 / Rrim(I) all: 0.741 / Rsym value: 0.631 / Net I/σ(I) obs: 2.6 / % possible all: 36.5

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Processing

Software
NameVersionClassification
REFMACv1.0refinement
XDSdata reduction
Aimless0.5.15data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MOH

5moh


Resolution: 1.31→54.33 Å / Cor.coef. Fo:Fc: 0.9572 / Cor.coef. Fo:Fc free: 0.9506 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.064 / SU Rfree Blow DPI: 0.062 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 3265 5.04 %RANDOM
Rwork0.1903 ---
obs0.1911 64749 86.36 %-
Displacement parametersBiso max: 107.73 Å2 / Biso mean: 22.36 Å2 / Biso min: 7.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.2814 Å20 Å20.6198 Å2
2--1.4235 Å20 Å2
3----1.1421 Å2
Refine analyzeLuzzati coordinate error obs: 0.178 Å
Refinement stepCycle: final / Resolution: 1.31→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 57 207 3012
Biso mean--26.48 26.99 -
Num. residues----327
LS refinement shellResolution: 1.31→1.34 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3205 117 5.05 %
Rwork0.2484 2199 -
all0.2518 2316 -
obs--86.36 %

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