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- PDB-8c5q: CK2 kinase bound to inhibitor AB668 -

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Basic information

Entry
Database: PDB / ID: 8c5q
TitleCK2 kinase bound to inhibitor AB668
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Kinase bivalent inhibitor
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / 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 proteasomal ubiquitin-dependent protein catabolic process / : / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / rhythmic process / double-strand break repair / kinase activity / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / regulation of cell cycle / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / 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-TL0 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKrimm, I. / Guichou, J.F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-21-CE18-0014-01 France
CitationJournal: To Be Published
Title: CK2 kinase bound to inhibitor AB668
Authors: Krimm, I. / Guichou, J.F.
History
DepositionJan 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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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)88,43321
Polymers85,5992
Non-polymers2,83419
Water97354
1
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,29111
Polymers42,8001
Non-polymers1,49110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,14210
Polymers42,8001
Non-polymers1,3439
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.521, 127.521, 125.065
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

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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: 42799.633 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

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Non-polymers , 5 types, 73 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TL0 / 2-methylpropyl 5-fluoranyl-3-[1-[[1-[2-[[4-(2-methylpropyl)phenyl]sulfonylamino]ethyl]piperidin-4-yl]methyl]-1,2,3-triazol-4-yl]-1~{H}-indole-2-carboxylate


Mass: 638.796 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H43FN6O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 33% polyethylene glycol methyl ether 5000, 0.2 M ammonium sulfate, 0.1 MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→51.64 Å / Num. obs: 36228 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 61.25 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 3561 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.09 Å / SU ML: 0.3174 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.5168
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2553 854 2.36 %
Rwork0.2154 35319 -
obs0.2164 36173 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.75 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 175 54 5765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815870
X-RAY DIFFRACTIONf_angle_d0.98167955
X-RAY DIFFRACTIONf_chiral_restr0.0546816
X-RAY DIFFRACTIONf_plane_restr0.00941059
X-RAY DIFFRACTIONf_dihedral_angle_d7.6293849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.33761410.29945806X-RAY DIFFRACTION99.98
2.66-2.860.29841390.27865779X-RAY DIFFRACTION99.87
2.86-3.150.31091410.25635832X-RAY DIFFRACTION99.92
3.15-3.610.28391410.2295856X-RAY DIFFRACTION99.88
3.61-4.540.22191430.18755915X-RAY DIFFRACTION99.7
4.54-45.090.23371490.19646131X-RAY DIFFRACTION99.13
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)
14.696729071560.3678448765231.675445111041.120535567660.6121847993142.849890088880.00730034184278-0.263696804204-0.1556282982230.340379493479-0.03616891397290.224266185990.373708957255-0.579252410741-0.002374946090950.534361210158-0.08996805619930.09174498234880.5077837615310.01086031569850.372995861096-2.57314917168-48.732699274415.3626212893
25.910728003113.35500167731-2.632729855134.24781385754-2.75340258931.82688308248-0.3832133334611.028090917450.4041624253-0.4985311538650.8030218821280.8357915608280.156829083394-1.27851426545-0.3462814393380.432587274746-0.100373820648-0.05724828761950.6848783042160.1250975994950.5753422918113.43645946364-32.49852214022.83100113396
31.76810287024-0.1895059535770.4516735197582.65763482085-0.4391811716462.62066402099-0.05087476362770.324672248440.20743116701-0.1390444265070.08653644222-0.1294457973180.1792613778690.0966247618841-0.0479893479920.353693476101-0.0845949933272-0.0007417595078140.463658712027-0.01004766568710.38558954828718.3877609876-39.51492089014.63286481675
41.420503959731.226825979461.057270909016.303952666774.075318354184.20694350483-0.03686382729830.235509308224-0.0223074057349-0.4042001849160.175431783545-0.471927101039-0.4832515053290.29114221607-0.158293201670.351011442738-0.0253345923474-0.007855607608720.45326177830.02379022686570.33518575046148.96729549312.84740183339-17.5353756554
53.935218064635.09767966379-1.850406958486.50989050623-2.25207487740.786057727360.988604748562-1.65649750773-0.09154802580261.50536296902-1.547677297710.381330053175-0.7968348741980.9542678898820.5014008483290.800556371691-0.1725060597270.07587379451940.990801250213-0.08422561523680.56521601570640.23112508073.38933599739-0.423096862764
61.547979569170.647159567555-0.5347447539332.74840399685-0.1465881584651.945583321480.0702194631132-0.352411976344-0.1279101852770.229230135279-0.0484797478923-0.04020567811860.006995550546750.166329040798-0.02551942680340.389207034923-0.0973046792855-0.02212813086920.579457463256-0.01727660872630.47338348256539.2855771854-16.1322310945-6.34565657266
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 113 )AA3 - 1131 - 111
22chain 'A' and (resid 114 through 149 )AA114 - 149112 - 147
33chain 'A' and (resid 150 through 331 )AA150 - 331148 - 329
44chain 'B' and (resid 2 through 108 )BG2 - 1081 - 107
55chain 'B' and (resid 109 through 129 )BG109 - 129108 - 128
66chain 'B' and (resid 130 through 332 )BG130 - 332129 - 331

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