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- PDB-3e3b: Crystal structure of catalytic subunit of human protein kinase CK... -

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Basic information

Entry
Database: PDB / ID: 3e3b
TitleCrystal structure of catalytic subunit of human protein kinase CK2alpha prime with a potent indazole-derivative inhibitor
ComponentsCasein kinase II subunit alpha'
KeywordsTRANSFERASE / Casein Kinase 2 / CK2alpha prime / CK2alpha inhibitor / selective kinase inhibitor / ATP-binding / Kinase / Nucleotide-binding / Polymorphism / Serine/threonine-protein kinase / Wnt signaling pathway
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-CCK / Casein kinase II subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKinoshita, T. / Nakaniwa, T. / Tada, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of human protein kinase CK2alpha2 with a potent indazole-derivative inhibitor
Authors: Nakaniwa, T. / Kinoshita, T. / Sekiguchi, Y. / Tada, T. / Nakanishi, I. / Kitaura, K. / Suzuki, Y. / Ohno, H. / Hirasawa, A. / Tsujimoto, G.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5362
Polymers40,1601
Non-polymers3761
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Casein kinase II subunit alpha'
hetero molecules

X: Casein kinase II subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0734
Polymers80,3202
Non-polymers7532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area3680 Å2
ΔGint-11 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.813, 102.126, 46.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Casein kinase II subunit alpha' / casein kinase CK2 alpha prime / CK II


Mass: 40159.984 Da / Num. of mol.: 1 / Fragment: residues in database 1-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A2, CK2A2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli)
References: UniProt: P19784, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CCK / [1-(6-{6-[(1-methylethyl)amino]-1H-indazol-1-yl}pyrazin-2-yl)-1H-pyrrol-3-yl]acetic acid


Mass: 376.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8% PEG8000, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→57.64 Å / Num. obs: 5978 / % possible obs: 100 % / Observed criterion σ(F): 0
Reflection shellResolution: 3.2→3.31 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PLK

1plk


Resolution: 3.2→57.64 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 -RANDOM
Rwork0.248 --
all0.268 --
obs0.268 5978 -
Refinement stepCycle: LAST / Resolution: 3.2→57.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 28 106 2938
Refine LS restraintsType: c_bond_d / Dev ideal: 0.008

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