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- PDB-9h9d: Protein kinase CK2 catalytic subunit alpha (CSNK2A1 gene product)... -

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Basic information

Entry
Database: PDB / ID: 9h9d
TitleProtein kinase CK2 catalytic subunit alpha (CSNK2A1 gene product) in complex the the indenoindole-type inhibitor MC11
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / Protein kinase / CK2 / Casein kinase II / inhibitor / ATP-competitive
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 / Maturation of hRSV A proteins ...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 / 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 / Wnt signaling pathway / Regulation of PTEN stability and activity / 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 / 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
: / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsNiefind, K. / Lindenblatt, D. / Werner, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
Citation
Journal: Biol.Chem. / Year: 2025
Title: Exploring the biological potential of the brominated indenoindole MC11 and its interaction with protein kinase CK2.
Authors: Marminon, C. / Werner, C. / Gast, A. / Herfindal, L. / Charles, J. / Lindenblatt, D. / Aichele, D. / Mularoni, A. / Doskeland, S.O. / Jose, J. / Niefind, K. / Le Borgne, M.
#1: Journal: Biol.Chem. / Year: 2025
Title: Exploring the biological potential of the brominated indenoindole MC11 and its interaction with protein kinase CK2
Authors: Marminon, C. / Werner, C. / Gast, A. / Herfindal, L. / Charles, J. / Lindenblatt, D. / Aichele, D. / Mularoni, A. / Doskeland, S.O. / Jose, J. / Niefind, K. / Le Borgne, M.
History
DepositionOct 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author

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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)85,32912
Polymers83,3712
Non-polymers1,95810
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-94 kcal/mol
Surface area30530 Å2
Unit cell
Length a, b, c (Å)128.317, 128.317, 125.707
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_1(chain "A" and (resid 2 through 227 or resid 229...
d_2ens_1(chain "B" and (resid 2 through 227 or resid 229...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERPHEPHEAA2 - 22716 - 241
d_12LYSLYSILEILEAA229 - 258243 - 272
d_13LYSLYSGLNGLNAA260 - 310274 - 324
d_14ARGARGLYSLYSAA312 - 329326 - 343
d_15A1ITGA1ITGA1ITGA1ITGAC401
d_21SERSERPHEPHEBB2 - 22716 - 241
d_22LYSLYSILEILEBB229 - 258243 - 272
d_23LYSLYSGLNGLNBB260 - 310274 - 324
d_24ARGARGLYSLYSBB312 - 329326 - 343
d_25A1ITGA1ITGA1ITGA1ITGBG401

NCS oper: (Code: givenMatrix: (0.0118264522894, -0.999884769647, 0.00951748147731), (0.996935118275, 0.0110543708493, -0.0774478588148), (0.0773337247009, 0.0104042449295, 0.996950975079)Vector: -62. ...NCS oper: (Code: given
Matrix: (0.0118264522894, -0.999884769647, 0.00951748147731), (0.996935118275, 0.0110543708493, -0.0774478588148), (0.0773337247009, 0.0104042449295, 0.996950975079)
Vector: -62.2474345188, 63.215267182, 33.2498289417)

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Components

#1: Protein Casein kinase II subunit alpha


Mass: 41685.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P68400
#2: Chemical ChemComp-A1ITG / 1,2,3,4-tetrakis(bromanyl)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione


Mass: 594.917 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H13Br4NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Reservoir: 0.2 M Lithium sulphate, 0.1 M BIS-TRIS-HCl, pH 6.5, 30 % PEG 3350 Inititial drop: 4 microliter CK2alpha 5 mg per mL incl. 1 mM MC11 in DMSO mixed with 2 microliter reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.82657 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82657 Å / Relative weight: 1
ReflectionResolution: 2.09→90.73 Å / Num. obs: 58978 / % possible obs: 94.5 % / Redundancy: 45.5 % / Biso Wilson estimate: 36.24 Å2 / CC1/2: 0.866 / Rmerge(I) obs: 1.335 / Rpim(I) all: 0.205 / Rrim(I) all: 1.352 / Net I/σ(I): 13.8
Reflection shellResolution: 2.09→2.166 Å / Redundancy: 40.5 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2949 / CC1/2: 0.538 / Rpim(I) all: 1.548 / Rrim(I) all: 10.506 / Rsym value: 10.327 / % possible all: 47.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
Cootmodel building
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→39.83 Å / SU ML: 0.2405 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.0356
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2288 1978 3.37 %
Rwork0.201 56742 -
obs0.202 58720 94.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.26 Å2
Refinement stepCycle: LAST / Resolution: 2.09→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 90 337 5969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00275827
X-RAY DIFFRACTIONf_angle_d0.64337906
X-RAY DIFFRACTIONf_chiral_restr0.0464805
X-RAY DIFFRACTIONf_plane_restr0.00511009
X-RAY DIFFRACTIONf_dihedral_angle_d13.89442188
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.861755062807 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.3432500.34441511X-RAY DIFFRACTION35.46
2.14-2.20.37951230.3023517X-RAY DIFFRACTION83.24
2.2-2.270.29911460.26134215X-RAY DIFFRACTION99.43
2.27-2.340.28261520.2344228X-RAY DIFFRACTION99.61
2.34-2.420.25281490.22124257X-RAY DIFFRACTION99.73
2.42-2.520.25611450.21494250X-RAY DIFFRACTION99.68
2.52-2.640.27181520.22074255X-RAY DIFFRACTION100
2.64-2.770.26091420.22894277X-RAY DIFFRACTION99.93
2.77-2.950.2621540.22244278X-RAY DIFFRACTION99.98
2.95-3.180.2321540.20474299X-RAY DIFFRACTION100
3.18-3.490.22361450.19834328X-RAY DIFFRACTION99.93
3.49-40.18251550.17134335X-RAY DIFFRACTION99.98
4-5.040.20831560.15924407X-RAY DIFFRACTION99.98
5.04-39.830.20561550.20494585X-RAY DIFFRACTION99.73
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)
11.14315581289-0.4470436210970.5661233775182.2721216069-0.6425243537471.89063636201-0.0809843993097-0.05089838231360.06773820631120.1518294628270.1060295154030.186801512288-0.262688913835-0.08653582065141.32033286325E-50.2564255965820.03717845359640.04064372777170.2701091961110.01088696012320.257232885437-49.29975487873.37627907655-14.0317346764
20.225989445094-0.212378445234-0.1813862776970.1367335602220.09598872253540.1038249992720.1083114128260.837453586676-0.01124196294-0.716547869356-0.3689855424150.0435558889313-0.0456632879046-0.294820351968-0.007904302227550.5973094400140.07122752864770.1090352595310.5730791670090.04243089718660.360070683093-40.93749419992.84662810148-30.9719384311
32.23307917055-0.743841619014-0.4872436699412.328929740580.4221196090372.101875211630.1140970377540.370152297737-0.120865620631-0.261476020644-0.04557049174170.03828948232610.0752205862584-0.09312654009580.001199371782660.2119165081150.0663954301951-0.02188556442640.278831546024-0.004055208017660.207482963679-39.6141201133-16.1487261426-25.2632892486
42.242084552070.5204814965861.058231235241.079876116410.4024401068521.611860917170.204436625091-0.0897413266082-0.1101855356980.0887514676039-0.1520596855340.1045085746230.15484410595-0.2248522081141.17508824991E-50.293925000597-0.01537096591050.04354088602160.3185793333650.02143739752120.290035614883-66.421030258415.131265866215.4615283656
50.08869419547730.1482694554290.005600838588030.183004393117-0.1280684439860.0437870729707-0.4169414448760.6081096694640.0635358190169-0.8036747649450.335398278625-0.1055610974010.0791390976021-0.147906647503-0.0007115403043570.590749075051-0.1272452533150.004148189218070.632667686330.07608497383730.453830706267-65.97632618524.8800880826-0.911534436803
61.763478269280.91451632041-0.4547893530131.71564655677-0.3135311628932.17649254468-0.1101764791610.2739265167240.0515255234027-0.1162102011190.15219180481-0.0257439392008-0.015599246930.115316175610.001054767274190.202612767586-0.06731313834140.01665931326190.2972317809010.0199422484480.259796200404-46.851377650925.55887822554.82706470402
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 108 )AA2 - 1081 - 107
22chain 'A' and (resid 109 through 129 )AA109 - 129108 - 128
33chain 'A' and (resid 130 through 329 )AA130 - 329129 - 328
44chain 'B' and (resid 2 through 108 )BC2 - 1081 - 107
55chain 'B' and (resid 109 through 129 )BC109 - 129108 - 128
66chain 'B' and (resid 130 through 329 )BC130 - 329129 - 328

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