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- PDB-6rcm: Human protein kinase CK2 alpha in complex with 2-cyano-2-propenam... -

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Basic information

Entry
Database: PDB / ID: 6rcm
TitleHuman protein kinase CK2 alpha in complex with 2-cyano-2-propenamide compound 3
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / kinase domain
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-K0N / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsDalle Vedove, A. / Zanforlin, E. / Ribaudo, G. / Zagotto, G. / Battistutta, R. / Lolli, G.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: A novel class of selective CK2 inhibitors targeting its open hinge conformation.
Authors: Dalle Vedove, A. / Zonta, F. / Zanforlin, E. / Demitri, N. / Ribaudo, G. / Cazzanelli, G. / Ongaro, A. / Sarno, S. / Zagotto, G. / Battistutta, R. / Ruzzene, M. / Lolli, G.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8626
Polymers40,1541
Non-polymers7095
Water6,630368
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-43 kcal/mol
Surface area15270 Å2
Unit cell
Length a, b, c (Å)58.371, 46.380, 63.449
Angle α, β, γ (deg.)90.000, 111.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40153.820 Da / Num. of mol.: 1 / Fragment: kinase domain (residues 1-337)
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-K0N / (~{E})-~{N}-(5-~{tert}-butyl-1,3,4-thiadiazol-2-yl)-2-cyano-3-(3-methoxy-4-oxidanyl-phenyl)prop-2-enamide


Mass: 358.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O3S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 38.01 % / Mosaicity: 0.18 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 32% PEG4000, 0.2 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→36.43 Å / Num. obs: 34812 / % possible obs: 99.7 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.035 / Rrim(I) all: 0.07 / Net I/σ(I): 14.2 / Num. measured all: 130311
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.733.90.7708818340.7520.4030.812.299.8
9-36.433.40.0238912590.9990.0140.02742.198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.7.1data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KWP

4kwp


Resolution: 1.7→36.429 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.75
RfactorNum. reflection% reflection
Rfree0.2012 1733 4.98 %
Rwork0.1612 --
obs0.1632 34786 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.59 Å2 / Biso mean: 25.3616 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: final / Resolution: 1.7→36.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 44 368 3185
Biso mean--32.1 35.42 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062965
X-RAY DIFFRACTIONf_angle_d0.8224030
X-RAY DIFFRACTIONf_chiral_restr0.054415
X-RAY DIFFRACTIONf_plane_restr0.005517
X-RAY DIFFRACTIONf_dihedral_angle_d7.9592461
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.750.31091400.25072736287699
1.75-1.80650.2651610.224827072868100
1.8065-1.87110.23861430.198627642907100
1.8711-1.9460.26411270.192327252852100
1.946-2.03460.25161380.1827442882100
2.0346-2.14180.23511310.164127652896100
2.1418-2.2760.19111270.165127542881100
2.276-2.45170.22541320.160427832915100
2.4517-2.69830.19281630.167327182881100
2.6983-3.08860.20451600.16172761292199
3.0886-3.89060.16561620.137327602922100
3.8906-36.43750.17441490.1412836298599
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)
10.1676-0.023-0.01890.0737-0.11640.6295-0.12530.1654-0.2142-0.0330.0937-0.11080.13530.0411-00.18930.01830.040.1439-0.06920.245115.5534-24.755-47.8884
20.38150.16940.06890.11870.12910.0983-0.00440.0691-0.08240.0233-0.0153-0.08010.01050.06110.00010.1291-0.0131-0.01470.1817-0.02790.166721.9993-13.8552-46.0202
30.05420.0078-0.0584-0.01630.00510.0795-0.05470.01610.16970.0652-0.0035-0.1382-0.19150.0478-0.00060.20420.0264-0.04290.1631-0.02230.247415.1242-3.8147-45.0618
40.98-0.0618-0.47230.3688-0.02120.2444-0.02740.0838-0.04160.060.0153-0.07490.0034-0.04980.00280.12370.0046-0.01270.0977-0.01280.1006-1.3759-14.415-39.4986
50.29890.0151-0.24290.19310.06680.27880.01510.28250.00130.04490.03370.0427-0.0219-0.32380.01040.11390.020.00460.19580.03240.1064-10.0026-8.7275-48.8131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 44 )A3 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 103 )A45 - 103
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 129 )A104 - 129
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 280 )A130 - 280
5X-RAY DIFFRACTION5chain 'A' and (resid 281 through 330 )A281 - 330

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