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- PDB-6l20: Crystal structure of CK2a2 with hematein -

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Basic information

Entry
Database: PDB / ID: 6l20
TitleCrystal structure of CK2a2 with hematein
ComponentsCasein kinase II subunit alpha'Casein kinase 2
KeywordsTRANSFERASE / protein kinase / inhibitor / complex
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 / negative regulation of apoptotic signaling pathway ...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 / 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-E3U / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08735128172 Å
AuthorsTsuyuguchi, M. / Kinoshita, T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Structural insights for producing CK2 alpha 1-specific inhibitors.
Authors: Tsuyuguchi, M. / Nakaniwa, T. / Hirasawa, A. / Nakanishi, I. / Kinoshita, T.
History
DepositionOct 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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'
D: Casein kinase II subunit alpha'
G: Casein kinase II subunit alpha'
J: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,39910
Polymers160,1274
Non-polymers1,2726
Water0
1
A: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3683
Polymers40,0321
Non-polymers3362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area14820 Å2
MethodPISA
2
D: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3683
Polymers40,0321
Non-polymers3362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area14530 Å2
MethodPISA
3
G: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3322
Polymers40,0321
Non-polymers3001
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15000 Å2
MethodPISA
4
J: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3322
Polymers40,0321
Non-polymers3001
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.7, 89.137, 95.994
Angle α, β, γ (deg.)81.154, 86.049, 90.063
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Casein kinase II subunit alpha' / Casein kinase 2 / CK II alpha'


Mass: 40031.855 Da / Num. of mol.: 4
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-E3U / (6aR)-3,4,6a,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2,1-c]chromen-9-one


Mass: 300.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 8000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.087→50 Å / Num. obs: 27801 / % possible obs: 91.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 48.1788392164 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.2
Reflection shellResolution: 3.09→3.14 Å / Rmerge(I) obs: 0.409 / Num. unique obs: 3582

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.9_1692+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E3B

3e3b


Resolution: 3.08735128172→35.0407993379 Å / SU ML: 0.506177809973 / Cross valid method: FREE R-VALUE / σ(F): 1.97272291486 / Phase error: 44.3696565227
RfactorNum. reflection% reflection
Rfree0.325917997517 2716 10.0158572113 %
Rwork0.240593441257 --
obs0.249340008441 27117 96.8637256653 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.8544976382 Å2
Refinement stepCycle: LAST / Resolution: 3.08735128172→35.0407993379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10744 0 2 0 10746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010825418122111025
X-RAY DIFFRACTIONf_angle_d1.3282693734214898
X-RAY DIFFRACTIONf_chiral_restr0.0501137155461543
X-RAY DIFFRACTIONf_plane_restr0.005593667927271885
X-RAY DIFFRACTIONf_dihedral_angle_d19.98337801394144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0874-3.14350.494425791911090.3635486998811119X-RAY DIFFRACTION83.0852503383
3.1435-3.20390.3733633872691630.3288379607251252X-RAY DIFFRACTION98.6750348675
3.2039-3.26920.4095050709091310.2947606956581306X-RAY DIFFRACTION97.8882833787
3.2692-3.34030.3492578551721450.2556535146971356X-RAY DIFFRACTION98.1687377371
3.3403-3.41790.3695585960631490.2644275146531267X-RAY DIFFRACTION98.7447698745
3.4179-3.50330.3053526689241270.2601786854751309X-RAY DIFFRACTION98.0204778157
3.5033-3.59790.352736125331510.2500200954571341X-RAY DIFFRACTION98.7425545996
3.5979-3.70370.3457261022611460.2515552564721301X-RAY DIFFRACTION98.9063568011
3.7037-3.82310.324535787891550.2466320869481293X-RAY DIFFRACTION98.6376021798
3.8231-3.95960.3211407395181340.2410066652631323X-RAY DIFFRACTION99.3860845839
3.9596-4.11790.3199991543581480.2160604911041293X-RAY DIFFRACTION98.8340192044
4.1179-4.30490.291849800711430.2196102388561363X-RAY DIFFRACTION99.4059405941
4.3049-4.53150.2951731216951290.2179837757841299X-RAY DIFFRACTION98.755186722
4.5315-4.81470.314401702661450.2158920230331325X-RAY DIFFRACTION99.0566037736
4.8147-5.18540.2821647284861410.2012070155491337X-RAY DIFFRACTION98.8628762542
5.1854-5.70520.2837970676811390.2032977267731300X-RAY DIFFRACTION99.2413793103
5.7052-6.52610.3354481123991780.223218433631293X-RAY DIFFRACTION99.3918918919
6.5261-8.20480.267504249561680.2343246652961293X-RAY DIFFRACTION99.3201903467
8.2048-35.040.3383113105461150.2395608194591031X-RAY DIFFRACTION77.4847870183

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