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- PDB-7z39: Structure of Belumosudil bound to CK2alpha -

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Basic information

Entry
Database: PDB / ID: 7z39
TitleStructure of Belumosudil bound to CK2alpha
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Kinase selectivity
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 / 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 ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / 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 / 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 / Chem-ICQ / PHOSPHATE ION / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBrear, P. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
University of Cambridge United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure of the Rho-associated coiled-coil kinase 2 inhibitor belumosudil bound to CK2 alpha.
Authors: Brear, P. / Hyvonen, M.
History
DepositionMar 1, 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_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 / _citation_author.identifier_ORCID
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

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8157
Polymers39,0311
Non-polymers7846
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-7 kcal/mol
Surface area15160 Å2
Unit cell
Length a, b, c (Å)58.508, 45.753, 63.462
Angle α, β, γ (deg.)90.000, 112.470, 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: K74A, K75A, K76A,
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ICQ / 2-[3-[4-(1~{H}-indazol-5-ylamino)quinazolin-2-yl]phenoxy]-~{N}-propan-2-yl-ethanamide


Mass: 452.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H24N6O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 107mM Mes pH 6.5, 29% glycerol ethoxylate, 1 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→50.52 Å / Num. obs: 39697 / % possible obs: 96.3 % / Redundancy: 11.6 % / Biso Wilson estimate: 19.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.021 / Rrim(I) all: 0.07 / Net I/σ(I): 20.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 15594 / CC1/2: 0.815 / Rpim(I) all: 0.253 / Rrim(I) all: 0.815 / % possible all: 76.7

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVH

5cvh


Resolution: 1.6→50.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.905 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 1985 5 %RANDOM
Rwork0.1638 ---
obs0.1662 37696 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.01 Å2 / Biso mean: 25.792 Å2 / Biso min: 11.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0.22 Å2
2---0.17 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: final / Resolution: 1.6→50.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 55 277 3081
Biso mean--42.68 34.26 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132957
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152717
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.6414017
X-RAY DIFFRACTIONr_angle_other_deg1.441.5946245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6255345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25721.404178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02415505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0741524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023545
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02735
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 134 -
Rwork0.246 2320 -
all-2454 -
obs--80.86 %

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