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

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Basic information

Entry
Database: PDB / ID: 6rfe
TitleHuman protein kinase CK2 alpha in complex with 2-cyano-2-propenamide compound 4
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 / 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-K0Z / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 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 13, 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)40,9477
Polymers40,1541
Non-polymers7946
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-39 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.200, 46.298, 62.997
Angle α, β, γ (deg.)90.000, 112.300, 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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-K0Z / (~{E})-~{N}-(5-bromanyl-1,3,4-thiadiazol-2-yl)-2-cyano-3-(3-methoxy-4-oxidanyl-phenyl)prop-2-enamide


Mass: 381.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9BrN4O3S
#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.: 361 / 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: 1.96 Å3/Da / Density % sol: 37.1 % / Mosaicity: 0 °
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: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.54→58.29 Å / Num. obs: 45232 / % possible obs: 98.1 % / Redundancy: 2.5 % / CC1/2: 0.978 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.035 / Rrim(I) all: 0.058 / Net I/σ(I): 12.4 / Num. measured all: 114548 / Scaling rejects: 352
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
1.54-1.572.30.281495521850.870.2210.3592.298.2
8.43-58.292.70.0227762900.9870.0170.02834.995

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KWP

4kwp


Resolution: 1.54→58.286 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.1975 2272 5.03 %
Rwork0.1716 --
obs0.1729 45167 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.19 Å2 / Biso mean: 24.1756 Å2 / Biso min: 8.19 Å2
Refinement stepCycle: final / Resolution: 1.54→58.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 45 361 3179
Biso mean--29.51 33.78 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062939
X-RAY DIFFRACTIONf_angle_d0.8653984
X-RAY DIFFRACTIONf_chiral_restr0.055410
X-RAY DIFFRACTIONf_plane_restr0.006511
X-RAY DIFFRACTIONf_dihedral_angle_d16.3191762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.54-1.57350.30011480.2356264498
1.5735-1.61010.28071290.2184265698
1.6101-1.65040.18481270.2066271399
1.6504-1.6950.27451430.1956266198
1.695-1.74490.25231280.1959268298
1.7449-1.80120.22151310.1971267598
1.8012-1.86560.22031470.1971271099
1.8656-1.94030.21231270.1882267398
1.9403-2.02860.21111320.1781269299
2.0286-2.13550.22151500.1789262696
2.1355-2.26930.18951700.1782261697
2.2693-2.44460.20151530.1748269498
2.4446-2.69060.22751490.1755267998
2.6906-3.07990.18881620.1648267397
3.0799-3.88020.16811440.1429271098
3.8802-58.280.15171320.1538279198
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)
12.2340.7113-0.44720.80740.08880.7824-0.1023-0.0068-0.02360.03010.0711-0.10240.10440.1440.03590.15730.0216-0.00430.1613-0.03710.190118.9733-18.4772-46.0647
21.59090.21970.50710.2433-0.44331.3989-0.1759-0.09550.23730.11430.0652-0.1384-0.1762-0.02130.04590.12420.0226-0.03960.1321-0.05030.18817.8635-11.9015-46.6761
31.5374-0.1954-0.83610.86170.08641.143-0.02310.10750.03550.0550.0379-0.0212-0.0034-0.0851-0.00790.08910.0049-0.01620.081-0.00760.0688-3.2618-13.0537-41.3256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 74 )A3 - 74
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 129 )A75 - 129
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 330 )A130 - 330

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