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- PDB-5csv: Crystal Structure of CK2alpha with Compound 6 bound -

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Basic information

Entry
Database: PDB / ID: 5csv
TitleCrystal Structure of CK2alpha with Compound 6 bound
ComponentsCasein kinase II subunit alphaCasein kinase 2
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 / 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 / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / 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 / 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
ACETATE ION / 3-AMINOBENZOIC ACID / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.375 Å
AuthorsBrear, P. / De Fusco, C. / Georgiou, K.H. / Spring, D. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust090340/Z/09/Z United Kingdom
CitationJournal: Chem Sci / Year: 2016
Title: Specific inhibition of CK2 alpha from an anchor outside the active site.
Authors: Brear, P. / De Fusco, C. / Hadje Georgiou, K. / Francis-Newton, N.J. / Stubbs, C.J. / Sore, H.F. / Venkitaraman, A.R. / Abell, C. / Spring, D.R. / Hyvonen, M.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2874
Polymers39,0311
Non-polymers2553
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint1 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.525, 45.433, 63.423
Angle α, β, γ (deg.)90.000, 111.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / CK II alpha


Mass: 39031.391 Da / Num. of mol.: 1 / Fragment: residues 2-329 / Mutation: R21S, K74A, K75A, K76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GAB / 3-AMINOBENZOIC ACID / GABACULINE / 3-Aminobenzoic acid


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.01 Å3/Da / Density % sol: 38.71 %
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: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.375→58.915 Å / Num. obs: 64289 / % possible obs: 99.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.35 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.018 / Rsym value: 0.028 / Net I/σ(I): 19 / Num. measured all: 207389
Reflection shellResolution: 1.375→1.38 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2 / Num. measured all: 43751 / Num. unique all: 15245 / CC1/2: 0.848 / Rpim(I) all: 0.235 / Rsym value: 0.449 / Rejects: 0 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNTrefinement
Aimless0.5.4data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAR

3war


Resolution: 1.375→58.91 Å / Cor.coef. Fo:Fc: 0.9638 / Cor.coef. Fo:Fc free: 0.9625 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.06 / SU Rfree Blow DPI: 0.059 / SU Rfree Cruickshank DPI: 0.058
RfactorNum. reflection% reflectionSelection details
Rfree0.195 3255 5.06 %RANDOM
Rwork0.1795 ---
obs0.1802 64271 97.46 %-
Displacement parametersBiso max: 99.19 Å2 / Biso mean: 25.17 Å2 / Biso min: 9.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20.7301 Å2
2---0.2057 Å20 Å2
3----0.6443 Å2
Refine analyzeLuzzati coordinate error obs: 0.156 Å
Refinement stepCycle: final / Resolution: 1.375→58.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 31 267 3046
Biso mean--28.43 32.97 -
Num. residues----327
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1021SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes441HARMONIC5
X-RAY DIFFRACTIONt_it2910HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion351SEMIHARMONIC5
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_contact3527SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d2910HARMONIC20.012
X-RAY DIFFRACTIONt_angle_deg3957HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion16.98
LS refinement shellResolution: 1.375→1.4 Å
RfactorNum. reflection% reflection
Rfree0.207 177 5.24 %
Rwork0.2124 3198 -
obs--97.46 %
Refinement TLS params.Method: refined / Origin x: 80.1535 Å / Origin y: 9.3185 Å / Origin z: 133.258 Å
111213212223313233
T-0.0041 Å2-0.0057 Å2-0.0089 Å2--0.0226 Å20.0033 Å2---0.0087 Å2
L0.1351 °20.0382 °2-0.024 °2-0.1502 °20.0954 °2--0.2102 °2
S0.02 Å °0.0192 Å °-0.011 Å °0.0543 Å °-0.0025 Å °-0.0551 Å °-0.0094 Å °0.0107 Å °-0.0175 Å °
Refinement TLS groupSelection details: { A|* }

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