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- PDB-7a49: Crystal structure of human protein kinase CK2alpha (CSNK2A1 gene ... -

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Basic information

Entry
Database: PDB / ID: 7a49
TitleCrystal structure of human protein kinase CK2alpha (CSNK2A1 gene product) in complex with the ATP-competitive inhibitor 6-bromo-5-chloro-1H-triazolo[4,5-b]pyridine
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2 / ATP-competitive inhibitor
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 / Maturation of hRSV A proteins / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC ...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 / Maturation of hRSV A proteins / 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 / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / 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 / negative regulation of translation / protein stabilization / 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 / 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
Similarity search - Domain/homology
Chem-QWN / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsNiefind, K. / Lindenblatt, D. / Toelzer, C. / Bretner, M. / Chojnacki, K. / Wielechowska, M. / Winska, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/4-2 Germany
Citation
Journal: Bioorg.Chem. / Year: 2021
Title: Synthesis, biological properties and structural study of new halogenated azolo[4,5-b]pyridines as inhibitors of CK2 kinase.
Authors: Chojnacki, K. / Lindenblatt, D. / Winska, P. / Wielechowska, M. / Toelzer, C. / Niefind, K. / Bretner, M.
#1: Journal: Bioorg. Chem. / Year: 2018
Title: Biological properties and structural study of new aminoalkyl derivatives of benzimidazole and benzotriazole, dual inhibitors of CK2 and PIM1 kinases.
Authors: Chojnacki, K. / Winska, P. / Wielechowska, M. / Lukowska-Chojnacka, E. / Toelzer, C. / Niefind, K. / Bretner, M.
#2: Journal: ACS Omega / Year: 2019
Title: Diacritic Binding of an Indenoindole Inhibitor by CK2alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2alpha' Structures.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Hochscherf, J. / Witulski, B. / Bouaziz, Z. / Marminon, C. / Bretner, M. / Le Borgne, M. / Jose, J. / Niefind, K.
#3: Journal: J. Med. Chem. / Year: 2020
Title: Structural and Mechanistic Basis of the Inhibitory Potency of Selected 2-Aminothiazole Compounds on Protein Kinase CK2.
Authors: Lindenblatt, D. / Nickelsen, A. / Applegate, V.M. / Jose, J. / Niefind, K.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Jan 31, 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)81,56114
Polymers80,1332
Non-polymers1,42812
Water3,945219
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7817
Polymers40,0671
Non-polymers7146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7817
Polymers40,0671
Non-polymers7146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.564, 127.564, 124.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERGLYA1 - 334
d_21ens_1SERGLYB1 - 334

NCS oper: (Code: givenMatrix: (0.00907483492286, -0.997387409777, 0.0716659067393), (0.999860108723, 0.00804359631376, -0.0146650448974), (0.0140502795212, 0.0717889641657, 0.997320878288)Vector: -64. ...NCS oper: (Code: given
Matrix: (0.00907483492286, -0.997387409777, 0.0716659067393), (0.999860108723, 0.00804359631376, -0.0146650448974), (0.0140502795212, 0.0717889641657, 0.997320878288)
Vector: -64.5858753792, -62.157919003, 33.2130198528)

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Components

#1: Protein Casein kinase II subunit alpha / Casein kinase 2 / 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 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-QWN / 6-bromanyl-5-chloranyl-1~{H}-[1,2,3]triazolo[4,5-b]pyridine


Mass: 233.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H2BrClN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 ...Details: 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 25 % PEG3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS BUFFER, PH 5.5) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST THE RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.028→89.135 Å / Num. obs: 60321 / % possible obs: 90 % / Redundancy: 13.1 % / Biso Wilson estimate: 49.51 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Rsym value: 0.077 / Net I/σ(I): 17.9
Reflection shellResolution: 2.028→2.136 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.827 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3018 / CC1/2: 0.563 / Rpim(I) all: 0.525 / Rrim(I) all: 1.892 / Rsym value: 1.827 / % possible all: 31.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 2.03→89.13 Å / SU ML: 0.2677 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2159 1203 2 %
Rwork0.189 59079 -
obs0.1896 60282 89.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.21 Å2
Refinement stepCycle: LAST / Resolution: 2.03→89.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5634 0 72 219 5925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025848
X-RAY DIFFRACTIONf_angle_d0.50187914
X-RAY DIFFRACTIONf_chiral_restr0.0438810
X-RAY DIFFRACTIONf_plane_restr0.0031012
X-RAY DIFFRACTIONf_dihedral_angle_d14.59822192
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.15500035223 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.110.2745290.28391384X-RAY DIFFRACTION19.33
2.11-2.20.29781320.2656428X-RAY DIFFRACTION89.42
2.2-2.320.27271450.23957216X-RAY DIFFRACTION99.99
2.32-2.470.28431470.22167208X-RAY DIFFRACTION99.99
2.47-2.660.22381480.2237258X-RAY DIFFRACTION99.99
2.66-2.920.261500.22137254X-RAY DIFFRACTION100
2.92-3.350.22641510.20067307X-RAY DIFFRACTION100
3.35-4.220.18951470.17187378X-RAY DIFFRACTION100
4.22-89.130.19691540.16657646X-RAY DIFFRACTION99.48
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)
12.89085523208-0.6920728835751.573580413620.891642050609-0.5200500802392.47669254482-0.03096002703090.113933764548-0.139402384206-0.169119115709-0.02589540797-0.1340705404060.2533118525730.329155543537-0.0001724568555460.5138882053450.01897474295340.05357188791090.4745339606030.01995736771510.4194129874572.43807285433-47.330043212618.2082857115
21.74718453994-0.6109967971080.02281865397711.665952490090.1606043764771.77784491256-0.0895975973448-0.174431623550.04728431974140.087405524790.1005850557530.01942806779410.1332633336090.007611134920779.53454041877E-60.4569889817720.0246620875476-0.02310965245110.4511763672450.008096873284780.426043484301-16.7628525222-39.727494340726.8984796669
30.776309389016-1.07330542086-0.03148757902631.52100588929-0.278281132532.444327062990.003805495936250.004349704088650.211190990624-0.268521916363-0.0160454734118-0.345932100919-0.4500070650360.124743837513-9.82419063265E-50.5880309513930.0110301679046-0.03467157492680.5502945878720.009832890968080.633055141685-13.6945941338-26.211255490621.8075801128
40.3560396255240.307958705602-0.03437137111830.4008075228990.04332620392571.86997829032-0.1268740108940.4539122065280.0570977720979-0.6215445531060.177461259168-0.062819516658-0.08202186113510.09689100025320.008182543994850.470879186156-0.003635561195870.02191200508360.517495411841-0.08829451012760.506273284646-18.0538350006-71.147026657935.7345808027
51.626878821660.962357476624-0.1801566189721.127001238330.7714571095071.424814600210.309589916918-0.163220991156-0.176149823555-0.461061784586-0.3592697835010.06997653681440.1565108392840.507895522964-0.0008303500985120.6991931986960.00559446101563-0.08547242045720.498674136644-0.0383083017090.531876730945-12.4498936126-50.035031900556.6161717371
61.36233925830.7250228717210.6753832973522.06721029835-0.5412215436342.08677159728-0.05159851170970.249475718095-0.0527877577137-0.0101607269579-0.00708780141203-0.336786958477-0.1771121956710.234766379122-0.0003137117871020.367042429963-0.0245982153737-0.01491495894350.438620813302-0.03441548373150.473055688429-13.3851012181-57.858780631746.1493974768
70.3482137399830.443991683360.05606073404120.2700219333780.08438995075840.006499505852410.342800008165-0.71432258793-0.05137620917750.81362831749-0.583309328335-0.212769552024-0.548133459104-0.127831421757-9.37099390635E-50.798764076631-0.1346937832660.04365109751730.818157974891-0.07061360902440.531510916011-23.0761570301-60.76423651961.0249138946
81.825582908090.391019843351-0.6262500215712.69308466979-0.6053785526891.661848515130.0841123526498-0.1901419116990.05770491157460.2327245938690.0010235967498-0.236526742742-0.1720033790150.186382672764-3.37792737186E-50.391786141617-0.045867658692-0.057378269380.455238371034-0.09190317479020.459115509816-22.3924615565-75.004048632755.064394596
90.175427387923-0.0663322893180.08217053761940.877860988730.08941472388741.07571112514-0.260880659771-0.354897976276-0.7633871633570.271996257864-0.0255477283996-0.2724180666520.823632928202-0.0603673941942-0.007874812430440.5167030190640.0370712518641-0.04216390690990.4700612632420.008354910266940.702570156306-17.664848406-95.666705085856.6028934188
100.7747463421750.233528583191-0.1641109205150.785578419862-0.08643415412240.3949647565920.039445896779-0.6841339728-0.1254583203170.626620469417-0.1685325379320.3188933443630.15110436449-0.2846446307270.0001252360491690.617912274285-0.03593030452330.01594632064540.726299040051-0.01063603799060.538379042695-34.3542924909-82.250125142367.0302056193
111.740557496421.143957215320.1759023445341.03438425813-0.2700952009942.123189716770.1170831868340.2783718362270.2024003147370.071586812719-0.03943968763280.223864581664-0.161536563705-0.416603657176-6.47031126946E-50.47853932905-0.0366217992801-0.0192887488880.552573793943-0.0310203356340.576958782073-36.9525513-76.27400211352.8538584381
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 129 )AA2 - 1291 - 128
22chain 'A' and (resid 130 through 304 )AA130 - 304129 - 303
33chain 'A' and (resid 305 through 335 )AA305 - 335304 - 334
44chain 'B' and (resid 2 through 35 )BB2 - 351 - 34
55chain 'B' and (resid 36 through 62 )BB36 - 6235 - 61
66chain 'B' and (resid 63 through 108 )BB63 - 10862 - 107
77chain 'B' and (resid 109 through 129 )BB109 - 129108 - 128
88chain 'B' and (resid 130 through 249 )BB130 - 249129 - 248
99chain 'B' and (resid 250 through 280 )BB250 - 280249 - 279
1010chain 'B' and (resid 281 through 304 )BB281 - 304280 - 303
1111chain 'B' and (resid 305 through 335 )BB305 - 335304 - 334

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