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- PDB-5cqu: Monoclinic Complex Structure of Protein Kinase CK2 Catalytic Subu... -

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Basic information

Entry
Database: PDB / ID: 5cqu
TitleMonoclinic Complex Structure of Protein Kinase CK2 Catalytic Subunit with a Benzotriazole-Based Inhibitor Generated by click-chemistry
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / ATP-COMPETITIVE INHIBITOR / Protein kinase CK2 / casein kinase 2
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 / kinase activity / KEAP1-NFE2L2 pathway / 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
Chem-JRJ / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsNiefind, K. / Schnitzler, A. / Swider, R. / Maslyk, M. / Ramos, A.
Funding support Germany, Spain, 2items
OrganizationGrant numberCountry
German Research FoundationNI 643/4-1 Germany
Spanish Ministry of Science and InnovationCTQ2011-24741 Spain
Citation
Journal: Rsc Adv / Year: 2015
Title: Synthesis, Biological Activity and Structural Study of New Benzotriazole-Based Protein Kinase CK2 Inhibitors
Authors: Swider, R. / Maslyk, M. / Zapico, J.M. / Coderch, C. / Panchuk, R. / Skorokhyd, N. / Schnitzler, A. / Niefind, K. / de Pascual-Teresa, B. / Ramos, A.
#1: Journal: Mol. Cell. Biochem. / Year: 2011
Title: MULTISITE-DIRECTED INHIBITORS OF PROTEIN KINASE CK2: NEW CHALLENGES
Authors: Swider, R. / Maslyk, M. / Martin-Santamaria, S. / Ramos, A. / de Pascual-Teresa, B.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBE
SupersessionSep 9, 2015ID: 4BXB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 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)41,1367
Polymers40,0671
Non-polymers1,0696
Water2,126118
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-29 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.481, 46.894, 63.464
Angle α, β, γ (deg.)90.00, 111.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40066.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: PT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-JRJ / 4-[4-[2-[4,5,6,7-tetrakis(bromanyl)benzotriazol-2-yl]ethyl]-1,2,3-triazol-1-yl]butan-1-amine


Mass: 600.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15Br4N7
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein solution: 6 mg/ml CK2alpha, 0.44 mM AMPPNP, 0.89 mM magnesium chloride, 250 mM NaCl, 12.5 mM Tris/HCl, pH 8.5; Reservoir: 30%(w/v) PEG4000, 0.2 M Lithiumsulfate, 0.1 M Tris/HCL, pH 8. ...Details: Protein solution: 6 mg/ml CK2alpha, 0.44 mM AMPPNP, 0.89 mM magnesium chloride, 250 mM NaCl, 12.5 mM Tris/HCl, pH 8.5; Reservoir: 30%(w/v) PEG4000, 0.2 M Lithiumsulfate, 0.1 M Tris/HCL, pH 8.5; the inhibitor JRJ was introduced by extensive soaking for one week

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→35.52 Å / Num. obs: 13511 / % possible obs: 99.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 13.4
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1936 / Rsym value: 0.372 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pvr

2pvr


Resolution: 2.35→35.516 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 668 4.94 %random
Rwork0.196 ---
obs0.1988 13511 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→35.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 53 118 2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022905
X-RAY DIFFRACTIONf_angle_d0.5123928
X-RAY DIFFRACTIONf_dihedral_angle_d11.7261096
X-RAY DIFFRACTIONf_chiral_restr0.023401
X-RAY DIFFRACTIONf_plane_restr0.002500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.53150.32331280.2492520X-RAY DIFFRACTION99
2.5315-2.78610.32391510.25712543X-RAY DIFFRACTION100
2.7861-3.1890.30881270.23152549X-RAY DIFFRACTION100
3.189-4.0170.25211280.17512584X-RAY DIFFRACTION100
4.017-35.52030.19491340.17022647X-RAY DIFFRACTION100
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)
11.8030.01540.07121.005-0.56781.00050.04570.097-0.27580.1544-0.0146-0.14510.29370.35560.00010.5127-0.00540.05840.5732-0.15380.52377.1194-16.1978-16.7454
21.55391.14240.14721.2034-0.66391.9635-0.17350.10960.25690.35630.1426-0.3687-0.10340.110700.46360.048-0.05390.4411-0.10420.47945.5749-9.5891-17.5143
32.22690.0161-1.23351.2123-0.24381.99130.00460.0616-0.13260.15080.068-0.16060.07030.1027-00.3590.0206-0.05110.3094-0.01510.3106-13.4669-12.1675-10.1708
41.81310.24650.0351.0557-0.55611.46980.05520.4870.1936-0.23260.22540.1144-0.1345-0.53290.00590.39470.0450.01640.49610.0380.3979-22.2468-6.3497-19.2228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 281 )
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 329 )

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