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- PDB-5ts8: Z. MAYS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETIT... -

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Basic information

Entry
Database: PDB / ID: 5ts8
TitleZ. MAYS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 5,6-DIBROMOBENZOTRIAZOLE
ComponentsProtein kinase CK2 catalytic subunit CK2 alpha-3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CK2 / CASEIN KINASE 2 / INHIBITOR / BROMO-BENZOTRIAZOLE / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / HALOGEN BOND
Function / homology
Function and homology information


protein kinase CK2 complex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity ...protein kinase CK2 complex / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / nucleus / 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
5,6-DIBROMOBENZOTRIAZOLE / ACETATE ION / BETA-MERCAPTOETHANOL / FORMIC ACID / L(+)-TARTARIC ACID / Casein kinase II subunit alpha / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWiniewska, M. / Kucinska, K. / Czapinska, H. / Piasecka, A. / Bochtler, M. / Poznanski, J.
Funding support Poland, 2items
OrganizationGrant numberCountry
NCN2012/07/B/ST4/01334 Poland
European Union283570
Citation
Journal: To Be Published
Title: STRUCTURAL AND THERMODYNAMIC ANALYSIS OF 5,6-DIBROMOBENZOTRIAZOLE BINDING TO CASEIN KINASE 2 ALPHA
Authors: Winiewska, M. / Kucinska, K. / Czapinska, H. / Piasecka, A. / Bochtler, M. / Poznanski, J.
#1: Journal: Biochim. Biophys. Acta / Year: 2015
Title: Thermodynamics parameters for binding of halogenated benzotriazole inhibitors of human protein kinase CK2alpha.
Authors: Winiewska, M. / Kucinska, K. / Makowska, M. / Poznanski, J. / Shugar, D.
#2: Journal: Biochem. Biophys. Res. Commun. / Year: 2015
Title: Thermodynamic parameters for binding of some halogenated inhibitors of human protein kinase CK2.
Authors: Winiewska, M. / Makowska, M. / Maj, P. / Wielechowska, M. / Bretner, M. / Poznanski, J. / Shugar, D.
History
DepositionOct 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: Protein kinase CK2 catalytic subunit CK2 alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,49111
Polymers40,4361
Non-polymers1,05510
Water8,161453
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint11 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.311, 59.726, 105.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein kinase CK2 catalytic subunit CK2 alpha-3


Mass: 40436.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FQF5, UniProt: P28523*PLUS

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Non-polymers , 9 types, 463 molecules

#2: Chemical ChemComp-7M0 / 5,6-DIBROMOBENZOTRIAZOLE / DIBROMO-2-BENZOTRIAZOLE


Mass: 276.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3Br2N3
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ACTIVE FORM OF THE PROTEIN KINASE CK2 IS HETEROTETRAMERIC AND COMPOSED OF TWO ALPHA SUBUNITS ...THE ACTIVE FORM OF THE PROTEIN KINASE CK2 IS HETEROTETRAMERIC AND COMPOSED OF TWO ALPHA SUBUNITS AND TWO BETA SUBUNITS. THE CRYSTAL STRUCTURE COMPRISES ONE ALPHA SUBUNIT ONLY.

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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: 43.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: pH 7.5 (1M Sodium HEPES; MOPS), 40% v/v PEG 500* MME; 20 % w/v PEG 20K; 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate ...Details: pH 7.5 (1M Sodium HEPES; MOPS), 40% v/v PEG 500* MME; 20 % w/v PEG 20K; 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9116 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.45→51.96 Å / Num. obs: 60461 / % possible obs: 98 % / Redundancy: 3.23 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Rsym value: 0.048 / Net I/σ(I): 14.19
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 2.78 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.81 / CC1/2: 0.84 / % possible all: 95.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREPphasing
WARPmodel building
REFMAC5.8.0103refinement
ARP/wARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RLK

4rlk


Resolution: 1.45→51.96 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.551 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS HAS BEEN USED AND U VALUES GENERATED WITH TLS CONTRIBUTION ADDED. DIFFERENCE DENSITY NEXT TO THE OH OXYGEN ATOM OF TYR257 AND TYR26 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS HAS BEEN USED AND U VALUES GENERATED WITH TLS CONTRIBUTION ADDED. DIFFERENCE DENSITY NEXT TO THE OH OXYGEN ATOM OF TYR257 AND TYR26 MIGHT INDICATE THE X-RAY RADIATION INDUCED HYDROPEROXIDE FORMATION. THE COMPLICATED COMPOSITION OF THE CRYSTALLIZATION BUFFER PRECLUDED UNAMBIGUOUS IDENTIFICATION OF THE LIGANDS. IN SOME CASES MIXTURES OF DIFFERENT COMPOUNDS ARE POSSIBLE EG TARTRATE, OXAMATE, ACETATE (AND DMSO), IN OTHER CASES THE LIGAND IDENTITY COULD NOT BE GUESSED AND THE DIFFERENCE DENSITY COULD AT BEST BE MODELLED AS A SET OF DISORDERED WATER MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.16945 2923 4.8 %RANDOM
Rwork0.14888 ---
obs0.14989 57482 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.744 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å2-0 Å2
2---0.9 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.45→51.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 60 453 3287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193460
X-RAY DIFFRACTIONr_bond_other_d0.0020.023287
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9664729
X-RAY DIFFRACTIONr_angle_other_deg0.9723.0017610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4255437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19924.034176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20615636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4181525
X-RAY DIFFRACTIONr_chiral_restr0.1030.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214102
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02843
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3171.8411607
X-RAY DIFFRACTIONr_mcbond_other1.3171.8411607
X-RAY DIFFRACTIONr_mcangle_it2.2092.7482082
X-RAY DIFFRACTIONr_mcangle_other2.2082.7522083
X-RAY DIFFRACTIONr_scbond_it1.5322.0961853
X-RAY DIFFRACTIONr_scbond_other1.5312.0961853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5893.0412645
X-RAY DIFFRACTIONr_long_range_B_refined5.96415.9544411
X-RAY DIFFRACTIONr_long_range_B_other5.48914.974156
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.449→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 183 -
Rwork0.337 3952 -
obs--92.11 %
Refinement TLS params.Method: refined / Origin x: 14.1582 Å / Origin y: 13.1883 Å / Origin z: 27.5611 Å
111213212223313233
T0.004 Å2-0.0032 Å2-0.0024 Å2-0.0086 Å2-0.0034 Å2--0.0082 Å2
L0.2781 °20.0317 °20.0458 °2-0.2046 °20.0765 °2--0.0403 °2
S0.0112 Å °-0.035 Å °0.0007 Å °-0.0086 Å °-0.0188 Å °0.0273 Å °-0.0056 Å °-0.006 Å °0.0076 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 338
2X-RAY DIFFRACTION1A401 - 410

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