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- PDB-6rb1: Human protein kinase CK2 alpha in complex with 2-cyano-2-propenam... -

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Basic information

Entry
Database: PDB / ID: 6rb1
TitleHuman protein kinase CK2 alpha in complex with 2-cyano-2-propenamide compound 1
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / kinase domain
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 / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-JWQ / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsBattistutta, 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 8, 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)40,9367
Polymers40,1541
Non-polymers7836
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-41 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.125, 46.455, 62.949
Angle α, β, γ (deg.)90.000, 111.940, 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
Details: kinase domain / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 370.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9F3N4O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2 Å3/Da / Density % sol: 38.54 % / Mosaicity: 0.09 °
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-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→46.46 Å / Num. obs: 50049 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.028 / Rrim(I) all: 0.065 / Net I/σ(I): 15.6 / Num. measured all: 262057 / Scaling rejects: 2
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
1.5-1.5350.6611225524460.7480.3240.7392.299.9
8.22-46.464.90.02416323350.9990.0120.02753.198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KWP

4kwp


Resolution: 1.5→36.353 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.21
RfactorNum. reflection% reflection
Rfree0.1902 2573 5.14 %
Rwork0.1652 --
obs0.1665 50031 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.54 Å2 / Biso mean: 24.5243 Å2 / Biso min: 8.48 Å2
Refinement stepCycle: final / Resolution: 1.5→36.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 48 310 3137
Biso mean--32.91 34.11 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072927
X-RAY DIFFRACTIONf_angle_d1.083964
X-RAY DIFFRACTIONf_chiral_restr0.043406
X-RAY DIFFRACTIONf_plane_restr0.005507
X-RAY DIFFRACTIONf_dihedral_angle_d14.9581104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.52890.26921390.244526112750
1.5289-1.56010.23271630.224225942757
1.5601-1.5940.23451270.213626322759
1.594-1.63110.2691310.211126202751
1.6311-1.67190.20231490.198426112760
1.6719-1.71710.23881350.192126352770
1.7171-1.76760.18821370.185726202757
1.7676-1.82460.22251150.180626812796
1.8246-1.88990.19411180.169126392757
1.8899-1.96550.22071540.171426132767
1.9655-2.0550.1921490.166526302779
2.055-2.16330.18341390.163926352774
2.1633-2.29880.2021490.160926282777
2.2988-2.47630.20471440.160626272771
2.4763-2.72540.20511670.167526442811
2.7254-3.11960.18591450.159326652810
3.1196-3.92960.16191530.144926592812
3.9296-36.36340.15911590.149627142873
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)
10.604-0.377-0.70120.59840.80371.6191-0.2962-0.1326-0.43220.02950.07690.16810.46120.06810.02740.28110.01370.0680.15120.07190.2724-9.239-8.535-10.6961
20.6757-0.96730.29182.06360.12031.6762-0.2372-0.0032-0.28880.01250.25680.15760.129-0.5046-0.00540.1706-0.06230.02280.22180.08250.3398-33.56027.101-11.4591
32.4385-0.82590.3931.2204-0.5380.75370.00740.0275-0.0874-0.10090.01710.2057-0.0079-0.202-0.00690.1080.0029-0.01740.18730.02350.1754-28.31159.8235-13.1472
41.69160.6133-0.14480.62290.54461.1768-0.1139-0.17650.2928-0.13770.17040.2175-0.28810.1247-0.05110.1862-0.0335-0.01470.15510.01430.1568-11.784218.214-8.0643
52.15920.1725-1.08070.5389-0.13921.259-0.07050.0382-0.0038-0.10690.04570.03370.0627-0.02640.01750.1188-0.0146-0.03020.06970.01110.0868-3.89048.5807-21.5768
60.93360.2712-0.40891.29140.16041.32250.0702-0.31980.10110.01620.0128-0.0532-0.13580.3303-0.07490.1133-0.03190.00360.2024-0.03170.11894.369815.1746-9.9631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )A2 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 44 )A25 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 108 )A45 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 149 )A109 - 149
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 280 )A150 - 280
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 330 )A281 - 330

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