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- PDB-2qc6: Protein kinase CK2 in complex with DBC -

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Basic information

Entry
Database: PDB / ID: 2qc6
TitleProtein kinase CK2 in complex with DBC
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE / CK2 / DBC / kinase inhibitors / coumarins
Function / homology
Function and homology information


protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / 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
3,8-DIBROMO-7-HYDROXY-4-METHYL-2H-CHROMEN-2-ONE / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBattistutta, R.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Coumarin as attractive casein kinase 2 (CK2) inhibitor scaffold: an integrate approach to elucidate the putative binding motif and explain structure-activity relationships.
Authors: Chilin, A. / Battistutta, R. / Bortolato, A. / Cozza, G. / Zanatta, S. / Poletto, G. / Mazzorana, M. / Zagotto, G. / Uriarte, E. / Guiotto, A. / Pinna, L.A. / Meggio, F. / Moro, S.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)39,6412
Polymers39,3071
Non-polymers3341
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.676, 60.252, 44.901
Angle α, β, γ (deg.)90.00, 103.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21A-470-

HOH

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Components

#1: Protein Casein kinase II subunit alpha / CK II / CK2-alpha


Mass: 39307.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-G12 / 3,8-DIBROMO-7-HYDROXY-4-METHYL-2H-CHROMEN-2-ONE / 3,8-DIBROMO-7-HYDROXY-4-METHYLCHROMEN-2-ONE


Mass: 333.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6Br2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 10-20% PEG4000, 0.2 M Sodium Acetate, 0.1 M Tris, pH 8, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→69 Å / Num. all: 31463 / Num. obs: 27834 / % possible obs: 86.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.85→1.94 Å / Rmerge(I) obs: 0.329 / % possible all: 57.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.261 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26831 1370 4.9 %RANDOM
Rwork0.21415 ---
all0.2168 29863 --
obs0.2168 26399 88.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.985 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å2-1.76 Å2
2--0.94 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 15 218 2961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222813
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9663805
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5885326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33123.862145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87115506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7121519
X-RAY DIFFRACTIONr_chiral_restr0.0930.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022152
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21402
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21924
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.71.51680
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12822643
X-RAY DIFFRACTIONr_scbond_it1.80131344
X-RAY DIFFRACTIONr_scangle_it2.5944.51162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 68 -
Rwork0.344 1265 -
obs--58.52 %

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