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- PDB-5m56: Monoclinic complex structure of human protein kinase CK2 catalyti... -

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Basic information

Entry
Database: PDB / ID: 5m56
TitleMonoclinic complex structure of human protein kinase CK2 catalytic subunit (isoform CK2alpha') with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21)
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / protein kinase CK2 / casein kinase 2
Function / homology
Function and homology information


regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins ...regulation of mitophagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Synthesis of PC / 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 / negative regulation of ubiquitin-dependent protein catabolic process / acrosomal vesicle / Signal transduction by L1 / liver regeneration / cerebral cortex development / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / spermatogenesis / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / chromatin / nucleoplasm / ATP binding / nucleus / 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-7FC / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.237 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 20, 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 2.0Oct 10, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
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'
B: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,78510
Polymers85,6442
Non-polymers1,1428
Water6,810378
1
A: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3014
Polymers42,8221
Non-polymers4793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4856
Polymers42,8221
Non-polymers6635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.341, 87.620, 72.977
Angle α, β, γ (deg.)90.00, 109.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42821.832 Da / Num. of mol.: 2 / Mutation: D39G, C336S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P19784, 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.: 2 / Source method: obtained synthetically / Formula: C16H8Cl2O5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PROTEIN STOCK SOLUTION: 5.5 MG/ML CK2ALPHA'-D39G-C336S 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 ...Details: PROTEIN STOCK SOLUTION: 5.5 MG/ML CK2ALPHA'-D39G-C336S 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: 25 % PEG4000, 15 % glycerol, 0.17 M sodium acetate, 0.08 M Tris/HCl, pH 8.5; DROP SOLUTION BEFORE EQULIBRATION: 0.3 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.3 MICROLITER RESERVOIR SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.237→44 Å / Num. obs: 39108 / % possible obs: 98 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09268 / Rsym value: 0.09268 / Net I/σ(I): 9.76
Reflection shellResolution: 2.237→2.317 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.6565 / Mean I/σ(I) obs: 1.78 / CC1/2: 0.685 / % possible all: 90

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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: 3OFM

3ofm


Resolution: 2.237→43.81 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 1161 2.97 %
Rwork0.1635 --
obs0.1648 39099 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.237→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5537 0 72 378 5987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025751
X-RAY DIFFRACTIONf_angle_d0.5167763
X-RAY DIFFRACTIONf_dihedral_angle_d11.6673436
X-RAY DIFFRACTIONf_chiral_restr0.042796
X-RAY DIFFRACTIONf_plane_restr0.003988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2373-2.33910.28251470.24364387X-RAY DIFFRACTION92
2.3391-2.46240.22251340.20944770X-RAY DIFFRACTION99
2.4624-2.61670.26131590.19864774X-RAY DIFFRACTION100
2.6167-2.81870.2371360.19314793X-RAY DIFFRACTION100
2.8187-3.10230.24581400.18024805X-RAY DIFFRACTION99
3.1023-3.5510.18931560.1594777X-RAY DIFFRACTION99
3.551-4.47320.17851480.12684768X-RAY DIFFRACTION99
4.4732-43.81840.17561410.14214864X-RAY DIFFRACTION99
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)
10.77030.28230.66961.0328-0.35643.7857-0.02960.02610.06760.07730.0014-0.0338-0.45350.08470.03840.33090.0140.0240.2323-0.00560.291917.35667.08438.6302
20.85410.04690.07521.23030.12612.53710.03160.0939-0.0731-0.12970.02660.01760.1383-0.1488-0.05350.294-0.001-0.02410.29120.02190.272511.5157-5.498623.0301
34.81862.25251.68752.15930.31612.99070.1243-0.2951-0.58260.2617-0.0413-0.25340.3978-0.0173-0.08130.4185-0.0163-0.01790.2510.05650.350917.7371-34.347776.0086
40.92371.35770.97536.1306-1.91183.8645-0.23240.0524-0.113-0.3580.1830.1167-0.1915-0.19080.03540.27260.01270.01880.3323-0.0230.34256.8745-16.73853.6308
53.0481-0.2640.19693.3417-0.27593.70470.00290.081-0.0056-0.2122-0.0310.39260.0454-0.27880.02910.2227-0.01960.01040.25670.00180.29389.2208-23.453259.5707
61.41580.08280.97531.4058-0.05151.984-0.081-0.00480.17060.2161-0.01120.0951-0.3111-0.03890.08770.33640.00850.01460.25290.00210.287419.5565-10.918468.4122
72.82940.75060.57991.0607-0.34761.70660.01770.0923-0.26230.14670.0024-0.16480.09220.105-0.02050.32530.0137-0.01750.2422-0.00870.262328.9813-25.096468.3126
82.8992-0.79220.21254.21321.18653.3545-0.05430.38190.1013-0.4446-0.1016-0.0008-0.33330.31740.14250.289-0.0458-0.03380.32970.03340.234940.5075-15.696863.3564
92.41970.92740.09614.18770.52162.5550.02070.1527-0.382-0.05760.1076-0.47950.32310.4611-0.10920.31860.033-0.08620.35160.02360.353447.0016-26.613470.3953
102.85390.15140.54132.95790.22652.929-0.0786-0.1780.20850.2614-0.0102-0.1188-0.21760.03790.07710.4136-0.0277-0.08130.2936-0.00870.257232.9287-9.951779.0692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 150 )
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 332 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 29 )
4X-RAY DIFFRACTION4chain 'B' and (resid 30 through 63 )
5X-RAY DIFFRACTION5chain 'B' and (resid 64 through 109 )
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 174 )
7X-RAY DIFFRACTION7chain 'B' and (resid 175 through 227 )
8X-RAY DIFFRACTION8chain 'B' and (resid 228 through 250 )
9X-RAY DIFFRACTION9chain 'B' and (resid 251 through 281 )
10X-RAY DIFFRACTION10chain 'B' and (resid 282 through 333 )

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