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- PDB-5m44: Complex structure of human protein kinase CK2 catalytic subunit w... -

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Basic information

Entry
Database: PDB / ID: 5m44
TitleComplex structure of human protein kinase CK2 catalytic subunit with a thieno[2,3-d]pyrimidin inhibitor 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 / 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 / positive regulation of Wnt signaling pathway / negative regulation of apoptotic 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-7EY / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.71 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 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 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

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Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5747
Polymers40,0671
Non-polymers5086
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-55 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.061, 72.061, 131.579
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-7EY / 3-[5-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]sulfanylpropanoic acid


Mass: 330.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2O2S2
#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.: 11 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
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: 4.2 M NaCl, 0.1 M sodium citrate, pH 5.0; 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.71→28 Å / Num. obs: 9935 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 15.75
Reflection shellResolution: 2.71→2.807 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.8084 / Mean I/σ(I) obs: 2.32 / CC1/2: 0.693 / % possible all: 98

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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: 3NSZ

3nsz


Resolution: 2.71→27.841 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.32
RfactorNum. reflection% reflection
Rfree0.2593 956 9.62 %
Rwork0.2186 --
obs0.2225 9935 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.71→27.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 27 11 2820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032881
X-RAY DIFFRACTIONf_angle_d0.5353897
X-RAY DIFFRACTIONf_dihedral_angle_d17.0091721
X-RAY DIFFRACTIONf_chiral_restr0.04401
X-RAY DIFFRACTIONf_plane_restr0.003501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7101-2.85290.35551360.31581228X-RAY DIFFRACTION98
2.8529-3.03140.33311500.27651229X-RAY DIFFRACTION100
3.0314-3.26520.26121080.25861284X-RAY DIFFRACTION100
3.2652-3.59310.26631340.22731267X-RAY DIFFRACTION100
3.5931-4.11160.25221260.19031291X-RAY DIFFRACTION100
4.1116-5.17480.21281490.1751300X-RAY DIFFRACTION100
5.1748-27.84230.24821530.20971380X-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)
10.78590.3341-0.60231.01220.16390.8617-0.392-0.05320.116-0.38320.25330.0118-0.2996-0.5632-0.29410.2890.18-0.04080.5211-0.03560.1782-2.155322.2033-29.7082
22.18320.2969-0.2041.0689-0.02771.2721-0.1618-0.2522-0.0560.6786-0.05790.1562-0.05-0.5142-0.11420.35130.1042-0.00470.3081-0.04430.1261-4.124918.8252-25.065
31.1034-0.21130.76291.89840.12942.10990.0296-0.0606-0.12110.07850.0896-0.73890.17480.0780.05260.17960.0246-0.04680.1197-0.0210.297916.7789.5187-21.8686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 331 )

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