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- PDB-3wik: Crystal structure of the CK2alpha/compound10 complex -

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Basic information

Entry
Database: PDB / ID: 3wik
TitleCrystal structure of the CK2alpha/compound10 complex
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE
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 / 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-LCT / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsKinoshita, T. / Nakaniwa, T. / Sekiguchi, Y. / Nakanishi, I.
CitationJournal: To be Published
Title: Identification of protein kinase CK2 inhibitors using solvent dipole ordering virtual screening
Authors: Nakanishi, I. / Murata, K. / Nagata, N. / Kurono, M. / Kinoshita, T. / Yasue, M. / Miyazaki, T. / Hirasawa, A. / Tsujimoto, G. / Kitaura, K.
History
DepositionSep 18, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)40,7422
Polymers40,4781
Non-polymers2641
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.382, 79.451, 82.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40478.191 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-335
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-LCT / N-[5-(4-nitrophenyl)-1,3,4-thiadiazol-2-yl]acetamide


Mass: 264.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N4O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% ethyleneglycol, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 11, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→57.03 Å / Num. obs: 27524 / % possible obs: 99.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.995→41.785 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 19.52 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2114 1145 5.12 %
Rwork0.1632 --
obs0.1656 22360 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.737 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--0.86 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.995→41.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 18 163 2991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172904
X-RAY DIFFRACTIONf_angle_d1.8523929
X-RAY DIFFRACTIONf_dihedral_angle_d14.381092
X-RAY DIFFRACTIONf_chiral_restr0.079405
X-RAY DIFFRACTIONf_plane_restr0.007506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.995-2.08570.2151650.17552538X-RAY DIFFRACTION98
2.0857-2.19570.20031270.162630X-RAY DIFFRACTION100
2.1957-2.33330.23881520.15782597X-RAY DIFFRACTION100
2.3333-2.51340.20821610.15222611X-RAY DIFFRACTION100
2.5134-2.76630.25091320.16022649X-RAY DIFFRACTION100
2.7663-3.16650.21181490.16232644X-RAY DIFFRACTION100
3.1665-3.98890.20281390.1562703X-RAY DIFFRACTION100
3.9889-41.79380.19641200.17352843X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -23.5789 Å / Origin y: -2.25 Å / Origin z: -10.5299 Å
111213212223313233
T0.1054 Å2-0.0012 Å2-0.0011 Å2-0.1004 Å20.01 Å2--0.1052 Å2
L0.5183 °20.1788 °2-0.1496 °2-0.4065 °2-0.0857 °2--0.4079 °2
S0.0297 Å °-0.0008 Å °-0.0055 Å °0.055 Å °-0.0267 Å °-0.0381 Å °0.0063 Å °-0.0061 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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