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- PDB-5m4i: Complex structure of human protein kinase CK2 catalytic subunit w... -

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Basic information

Entry
Database: PDB / ID: 5m4i
TitleComplex structure of human protein kinase CK2 catalytic subunit with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21) crystallized under high-salt conditions
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2
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 / 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 / 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-7FC / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.218 Å
AuthorsNiefind, K. / Bischoff, N. / Yarmoluk, S.M. / Bdzhola, V.G. / Golub, A.G. / Balanda, A.O. / Prykhod'ko, A.O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNI 643/4-2 Germany
Citation
Journal: Pharmaceuticals / Year: 2017
Title: Structural Hypervariability of the Two Human Protein Kinase CK2 Catalytic Subunit Paralogs Revealed by Complex Structures with a Flavonol- and a Thieno[2,3-d]pyrimidine-Based Inhibitor.
Authors: Niefind, K. / Bischoff, N. / Golub, A.G. / Bdzhola, V.G. / Balanda, A.O. / Prykhod'ko, A.O. / Yarmoluk, S.M.
#1: Journal: ACS Chem. Biol. / Year: 2015
Title: A Note of Caution on the Role of Halogen Bonds for Protein Kinase/Inhibitor Recognition Suggested by High- And Low-Salt CK2alpha Complex Structures.
Authors: Guerra, B. / Bischoff, N. / Bdzhola, V.G. / Yarmoluk, S.M. / Issinger, O.G. / Golub, A.G. / Niefind, K.
#2: Journal: Eur J Med Chem / Year: 2011
Title: Synthesis and biological evaluation of substituted (thieno[2,3-d]pyrimidin-4-ylthio)carboxylic acids as inhibitors of human protein kinase CK2.
Authors: Golub, A.G. / Bdzhola, V.G. / Briukhovetska, N.V. / Balanda, A.O. / Kukharenko, O.P. / Kotey, I.M. / Ostrynska, O.V. / Yarmoluk, S.M.
#3: Journal: Mol. Cell. Biochem. / Year: 2011
Title: Structure-based discovery of novel flavonol inhibitors of human protein kinase CK2.
Authors: Golub, A.G. / Bdzhola, V.G. / Kyshenia, Y.V. / Sapelkin, V.M. / Prykhod'ko, A.O. / Kukharenko, O.P. / Ostrynska, O.V. / Yarmoluk, S.M.
History
DepositionOct 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3May 17, 2017Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 17, 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)40,5957
Polymers40,0671
Non-polymers5286
Water1,982110
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-53 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.591, 72.591, 133.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 40066.742 Da / Num. of mol.: 1
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-7FC / 4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid


Mass: 351.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H8Cl2O5
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PROTEIN STOCK SOLUTION: 6 MG/ML CK2ALPHA1-335 IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5; INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO; PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER ...Details: PROTEIN STOCK SOLUTION: 6 MG/ML CK2ALPHA1-335 IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5; INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO; PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER PROTEIN STOCK SOLUTION + 10 MICROLITER INHIBITOR STOCK SOLUTION; RESERVOIR SOLUTION: 4.3 M NACL, 0.1 M SODIUM CITRATE, PH 5.2; DROP SOLUTION BEFORE EQULIBRATION: 0.5 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.5 MICROLITER RESERVOIR SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.218→49.1 Å / Num. obs: 18350 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 36.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1109 / Rsym value: 0.1109 / Net I/σ(I): 0.1109
Reflection shellResolution: 2.218→2.297 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.169 / Mean I/σ(I) obs: 1.84 / CC1/2: 0.616 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVR

2pvr


Resolution: 2.218→49.085 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.8
RfactorNum. reflection% reflection
Rfree0.2283 1034 5.64 %
Rwork0.1881 --
obs0.1904 18348 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.218→49.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 28 110 2936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022898
X-RAY DIFFRACTIONf_angle_d0.4653922
X-RAY DIFFRACTIONf_dihedral_angle_d20.1221730
X-RAY DIFFRACTIONf_chiral_restr0.042403
X-RAY DIFFRACTIONf_plane_restr0.003504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2181-2.33510.30151450.25552427X-RAY DIFFRACTION100
2.3351-2.48140.30341450.22452403X-RAY DIFFRACTION100
2.4814-2.6730.27421400.22582435X-RAY DIFFRACTION100
2.673-2.94190.27181360.21792457X-RAY DIFFRACTION100
2.9419-3.36750.23261500.19672453X-RAY DIFFRACTION100
3.3675-4.24240.19141420.15712506X-RAY DIFFRACTION100
4.2424-49.09720.20561760.16982633X-RAY DIFFRACTION100
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)
11.6301-0.39620.52813.5005-1.77214.218-0.0753-0.17280.03690.01260.07050.3356-0.4626-0.33510.00010.39910.0372-0.00760.3966-0.03780.3176-22.69652.765530.0114
20.8064-1.29-0.59082.32121.3070.93920.07350.68370.3144-1.06090.2226-0.5634-0.24010.26440.13020.6964-0.00320.09530.71570.03930.5382-12.21281.371714.6706
33.1479-0.31120.09811.37471.07292.58240.06850.259-0.1789-0.1433-0.0062-0.0659-0.07210.06810.00230.25440.02280.00370.32930.0130.3215-13.016-12.562422.6516
43.21860.1810.60653.1830.58952.36910.14270.2143-0.8111-0.03990.243-0.10890.29470.28890.01320.34670.0683-0.04430.4402-0.02340.5342-5.2614-22.688321.6493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 249 )
4X-RAY DIFFRACTION4chain 'A' and (resid 250 through 333 )

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