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- PDB-5cqw: Tetragonal Complex Structure of Protein Kinase CK2 Catalytic Subu... -

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Basic information

Entry
Database: PDB / ID: 5cqw
TitleTetragonal 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 / 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
Chem-JRJ / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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
Spanisch 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.
#2: Journal: J. Mol. Biol. / Year: 2003
Title: Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
Authors: Ermakova, I. / Boldyreff, B. / Issinger, O.G. / Niefind, K.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBE
SupersessionSep 9, 2015ID: 4bxa
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

Downloads & links

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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)82,83121
Polymers80,1332
Non-polymers2,69819
Water2,774154
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,46411
Polymers40,0671
Non-polymers1,39710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,36810
Polymers40,0671
Non-polymers1,3019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.092, 127.092, 126.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 40066.742 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 173 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C14H15Br4N7
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Protein solution: 6 mg/ml CK2alpha, 1 mM Inhibitor, 10 %(v/v) DMSO, 250 mM NaCl, 12.5 mM Tris/HCl, pH 8.5; Reservoir: 25 %(w/v) PEG 3350, 0.2 M Lithiumsulfate, 0.1 M Bis-Tris/HCl, pH 5.5; ...Details: Protein solution: 6 mg/ml CK2alpha, 1 mM Inhibitor, 10 %(v/v) DMSO, 250 mM NaCl, 12.5 mM Tris/HCl, pH 8.5; Reservoir: 25 %(w/v) PEG 3350, 0.2 M Lithiumsulfate, 0.1 M Bis-Tris/HCl, pH 5.5; drop: 1 Mikroliter pre-incubated CK2alpha/Inhibitor solution and 1 Mikroliter reservoir

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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: 2.65→44.93 Å / Num. obs: 30832 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 13.1
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.173 / Mean I/σ(I) obs: 2 / Rsym value: 1.173 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGA

3nga


Resolution: 2.65→44.934 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1547 5.03 %Random
Rwork0.1824 ---
obs0.1847 30757 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→44.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5586 0 131 154 5871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025878
X-RAY DIFFRACTIONf_angle_d0.5847954
X-RAY DIFFRACTIONf_dihedral_angle_d12.2612210
X-RAY DIFFRACTIONf_chiral_restr0.025808
X-RAY DIFFRACTIONf_plane_restr0.0021010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-2.73560.32731230.27662608X-RAY DIFFRACTION100
2.7356-2.83340.31711330.2582614X-RAY DIFFRACTION100
2.8334-2.94680.26971460.23352624X-RAY DIFFRACTION100
2.9468-3.08090.29231390.22192605X-RAY DIFFRACTION100
3.0809-3.24330.28351310.21212628X-RAY DIFFRACTION100
3.2433-3.44640.24341280.19442662X-RAY DIFFRACTION100
3.4464-3.71240.221620.17092602X-RAY DIFFRACTION100
3.7124-4.08570.21281370.1552666X-RAY DIFFRACTION100
4.0857-4.67640.2161430.13962668X-RAY DIFFRACTION100
4.6764-5.88970.18551550.15252693X-RAY DIFFRACTION100
5.8897-44.94020.19661500.18932840X-RAY DIFFRACTION99
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)
11.02220.05590.35630.6246-0.47832.8004-0.1337-0.03250.07040.55440.1948-0.22390.2577-0.021-0.00110.40250.0171-0.03630.4315-0.01250.455747.2131.522953.8991
21.1303-0.70950.28780.88680.51991.834-0.0794-0.0086-0.0689-0.2067-0.3013-0.06450.0422-0.53370.00080.46640.01530.04430.3441-0.08050.501451.409-9.736139.9925
30.5110.8151-0.03681.32980.16031.32750.02610.1648-0.27850.0716-0.2132-0.20030.102-0.03920.00010.37010.0543-0.03040.3531-0.01160.524949.5241-5.341250.2321
40.8914-1.00420.61551.1311-0.69380.4240.39730.3687-0.2067-0.4004-0.23060.1874-0.0554-0.01230.00080.48370.1219-0.05430.5433-0.120.49435.56891.400136.566
51.5031-0.51120.29282.306-0.84352.44730.10510.45730.1882-0.299-0.1058-0.2463-0.21080.15920.00010.42120.12670.04720.50950.01710.452542.141817.489837.5281
61.0415-0.43480.19531.17280.28251.18050.2704-0.17080.0050.1582-0.1728-0.1542-0.2098-0.27110.01020.3710.17190.0150.5027-0.01950.400527.978214.289742.1323
70.5810.11620.27930.74060.18212.2715-0.1674-0.20080.04970.48410.2092-0.04970.3840.0974-0.00030.4910.014-0.01680.46630.02130.43847.18582.3343114.395
81.766-1.21730.20871.24980.68061.6629-0.1247-0.45080.49640.0423-0.13980.5674-0.05860.0201-0.00030.5374-0.06010.01390.3588-0.05240.484650.6026-9.1914100.1568
90.9524-0.44330.03932.71511.24130.97930.21040.3384-0.1726-0.2053-0.25670.0792-0.10730.2095-0.03430.50690.0901-0.02510.47110.03310.463645.3919-3.5349103.8394
102.0878-0.55860.25062.1388-0.21862.53190.24340.18260.0695-0.3542-0.17340.1105-0.1475-0.0489-0.00010.54770.14570.00060.3786-0.02730.38738.133216.652399.3906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 304 )
6X-RAY DIFFRACTION6chain 'A' and (resid 305 through 332 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 44 )
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 74 )
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 129 )
10X-RAY DIFFRACTION10chain 'B' and (resid 130 through 332 )

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