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- PDB-4kwp: Crystal Structure of Human CK2-alpha in complex with a benzimidaz... -

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Basic information

Entry
Database: PDB / ID: 4kwp
TitleCrystal Structure of Human CK2-alpha in complex with a benzimidazole inhibitor (K164) at 1.25 A resolution
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / phosphorylation / small molecule inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / rhythmic process / KEAP1-NFE2L2 pathway / 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-EXX / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsRanchio, A. / Lolli, G. / Battistutta, R.
CitationJournal: Cell.Mol.Life Sci. / Year: 2014
Title: Cell-permeable dual inhibitors of protein kinases CK2 and PIM-1: structural features and pharmacological potential.
Authors: Cozza, G. / Girardi, C. / Ranchio, A. / Lolli, G. / Sarno, S. / Orzeszko, A. / Kazimierczuk, Z. / Battistutta, R. / Ruzzene, M. / Pinna, L.A.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,60912
Polymers40,1541
Non-polymers1,45511
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.448, 45.821, 63.486
Angle α, β, γ (deg.)90.000, 111.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 40153.820 Da / Num. of mol.: 1 / Fragment: UNP residues 1-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P68400, non-specific serine/threonine protein kinase

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Non-polymers , 7 types, 475 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EXX / 4,5,6,7-tetrabromo-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-1H-benzimidazole / Tetrabromo-Deoxyribofuranosyl-Benzimidazole


Mass: 549.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10Br4N2O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 1.97 Å3/Da / Density % sol: 37.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris-HCl, 0.2 M lithium sulphate, 32% w/v PEG 4000, pH 8.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.91 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.25→59.211 Å / Num. obs: 86589 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→36.238 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8881 / SU ML: 0.12 / σ(F): 1.34 / Phase error: 18.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1696 4336 5.02 %RANDOM
Rwork0.1361 ---
obs0.1378 86380 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.58 Å2 / Biso mean: 19.9157 Å2 / Biso min: 6.13 Å2
Refinement stepCycle: LAST / Resolution: 1.25→36.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 74 464 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072977
X-RAY DIFFRACTIONf_angle_d1.1544034
X-RAY DIFFRACTIONf_chiral_restr0.073416
X-RAY DIFFRACTIONf_plane_restr0.006511
X-RAY DIFFRACTIONf_dihedral_angle_d14.0971136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.26420.2751480.217627042852100
1.2642-1.27910.24491510.214127362887100
1.2791-1.29470.28381430.202727132856100
1.2947-1.31110.23211550.207626922847100
1.3111-1.32830.25111470.190927292876100
1.3283-1.34650.24491230.1852732285599
1.3465-1.36580.24961400.178827022842100
1.3658-1.38620.23011450.169227372882100
1.3862-1.40780.24331210.166227302851100
1.4078-1.43090.20451270.164927612888100
1.4309-1.45560.19351460.151327072853100
1.4556-1.4820.17071510.145327322883100
1.482-1.51050.1941510.139627192870100
1.5105-1.54140.16721570.127627032860100
1.5414-1.57490.17921440.123827512895100
1.5749-1.61150.16341330.126727312864100
1.6115-1.65180.21641420.126927522894100
1.6518-1.69650.18341250.122327572882100
1.6965-1.74640.1631300.12082705283599
1.7464-1.80280.18351480.12022746289499
1.8028-1.86720.16071310.121227622893100
1.8672-1.9420.17391650.121927002865100
1.942-2.03030.14431510.116727232874100
2.0303-2.13740.12481590.112327432902100
2.1374-2.27130.15531510.11572681283298
2.2713-2.44660.15141450.12242739288499
2.4466-2.69270.17561390.137227662905100
2.6927-3.08220.16851510.13827782929100
3.0822-3.88260.14631720.127327612933100
3.8826-36.25280.15181450.144828522997100

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