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- PDB-5mow: Crystal Structure of CK2alpha with ZT0432 bound -

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Basic information

Entry
Database: PDB / ID: 5mow
TitleCrystal Structure of CK2alpha with ZT0432 bound
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 / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ACETATE ION / 5-bromopyridine-2,3-diamine / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsBrear, P. / De Fusco, C. / Georgiou, K. / Iegre, J. / Sore, H. / Hyvonen, M. / Spring, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust090340/Z/09/Z United Kingdom
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: A fragment-based approach leading to the discovery of a novel binding site and the selective CK2 inhibitor CAM4066.
Authors: De Fusco, C. / Brear, P. / Iegre, J. / Georgiou, K.H. / Sore, H.F. / Hyvonen, M. / Spring, D.R.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,2425
Polymers82,9362
Non-polymers3063
Water5,603311
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7153
Polymers41,4681
Non-polymers2472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5272
Polymers41,4681
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.402, 68.693, 335.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#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
#2: Chemical ChemComp-BR9 / 5-bromopyridine-2,3-diamine


Mass: 188.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6BrN3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.24 Å3/Da / Density % sol: 44.97 % / Mosaicity: 0.17 °
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: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.86→67.04 Å / Num. obs: 63101 / % possible obs: 99.8 % / Redundancy: 7.9 % / Biso Wilson estimate: 33.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.86-1.967.90.730.871199.9
5.88-67.047.80.0330.999199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.2.14data scaling
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVH

5cvh


Resolution: 1.86→55.87 Å / Cor.coef. Fo:Fc: 0.9418 / Cor.coef. Fo:Fc free: 0.9385 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.136 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.115
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 3197 5.07 %RANDOM
Rwork0.1899 ---
obs0.1906 63019 99.08 %-
Displacement parametersBiso max: 154.01 Å2 / Biso mean: 48.16 Å2 / Biso min: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.4188 Å20 Å20 Å2
2---9.8017 Å20 Å2
3---7.3829 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: final / Resolution: 1.86→55.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5500 0 17 311 5828
Biso mean--46.8 46.55 -
Num. residues----652
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2038SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes144HARMONIC2
X-RAY DIFFRACTIONt_gen_planes842HARMONIC5
X-RAY DIFFRACTIONt_it5736HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion691SEMIHARMONIC5
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_contact6452SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d5736HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg7767HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion16.5
LS refinement shellResolution: 1.86→1.9 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2341 227 5.35 %
Rwork0.2234 4013 -
obs--99.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2070.05990.13350.2937-0.15870.6950.0716-0.0550.03950.0266-0.07650.0035-0.01-0.01880.0049-0.0565-0.04770.0008-0.025-0.0224-0.028616.243144.4996356.6946
21.42950.1240.961800.29091.5109-0.1054-0.42890.0363-0.14690.0679-0.06880.0801-0.45690.0375-0.0349-0.0240.0250.1096-0.0191-0.1402-6.1783155.2618397.5218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 327
2X-RAY DIFFRACTION2{ B|* }B4 - 327

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