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- PDB-5oqu: The crystal structure of CK2alpha in complex with compound 5 -

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Basic information

Entry
Database: PDB / ID: 5oqu
TitleThe crystal structure of CK2alpha in complex with compound 5
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2alpha / CK2a / fragment based drug discovery / high concentration screening / selective ATP competitive inhibitors / surface entrophy reduction
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 / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 ...Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-A4B / ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.324 Å
AuthorsBrear, P. / De Fusco, C. / Iegre, J. / Yoshida, M. / Mitchell, S. / Rossmann, M. / Carro, L. / Sore, H. / Hyvonen, M. / Spring, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust090340/Z/09/Z United Kingdom
Wellcome Trust107714/Z/15/Z United Kingdom
CitationJournal: Chem Sci / Year: 2018
Title: Second-generation CK2 alpha inhibitors targeting the alpha D pocket.
Authors: Iegre, J. / Brear, P. / De Fusco, C. / Yoshida, M. / Mitchell, S.L. / Rossmann, M. / Carro, L. / Sore, H.F. / Hyvonen, M. / Spring, D.R.
History
DepositionAug 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / 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.name
Revision 2.0Oct 7, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / pdbx_validate_symm_contact / refine_hist / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_2 / _refine_hist.d_res_high / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Casein kinase II subunit alpha
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,07714
Polymers82,9362
Non-polymers2,14112
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-46 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.668, 67.922, 332.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-408-

IHP

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Components

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Protein , 1 types, 2 molecules BA

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


Mass: 41467.793 Da / Num. of mol.: 2
Fragment: residues 2-329 and N-terminal extension GSMDIEFDDDADDDGSGSGSGSGS
Mutation: R21S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase

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Non-polymers , 7 types, 27 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-A4B / [3-chloranyl-4-(2-methoxyphenyl)phenyl]methanamine


Mass: 247.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14ClNO
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.324→332.804 Å / Num. obs: 32253 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 59.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 18.4 / Num. measured all: 209930
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.324-2.3316.40.84420513210.8910.3590.9192.3
10.785-332.8044.80.02318643870.9990.010.02545.1

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
Aimlessdata scaling
PDB_EXTRACT3.23data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVH

5cvh


Resolution: 2.324→166.4 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.8967 / SU R Cruickshank DPI: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.381 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 1601 4.98 %RANDOM
Rwork0.2197 ---
obs0.2209 32179 99.38 %-
Displacement parametersBiso max: 178.93 Å2 / Biso mean: 73.53 Å2 / Biso min: 26.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.584 Å20 Å20 Å2
2---23.4728 Å20 Å2
3---21.8888 Å2
Refine analyzeLuzzati coordinate error obs: 0.345 Å
Refinement stepCycle: final / Resolution: 2.324→166.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 0 130 15 5625
Biso mean--90.82 51.3 -
Num. residues----648
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2079SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes144HARMONIC2
X-RAY DIFFRACTIONt_gen_planes879HARMONIC5
X-RAY DIFFRACTIONt_it5831HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion697SEMIHARMONIC5
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_contact6443SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5831HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7914HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion19.68
LS refinement shellResolution: 2.32→2.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3121 130 4.73 %
Rwork0.2543 2619 -
all0.2569 2749 -
obs--99.38 %

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