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- PDB-3u4u: Casein kinase 2 in complex with AZ-Inhibitor -

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Basic information

Entry
Database: PDB / ID: 3u4u
TitleCasein kinase 2 in complex with AZ-Inhibitor
ComponentsCasein kinase II subunit alphaCasein kinase 2
KeywordsTransferase/Transferase Inhibitor / Kinase / Transferase / Inhibitor binding / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / peptidyl-threonine phosphorylation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of cell population proliferation / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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-LNH / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLarsen, N.A. / Dowling, J.
CitationJournal: ACS Med Chem Lett / Year: 2012
Title: Potent and Selective Inhibitors of CK2 Kinase Identified through Structure-Guided Hybridization.
Authors: Dowling, J.E. / Chuaqui, C. / Pontz, T.W. / Lyne, P.D. / Larsen, N.A. / Block, M.H. / Chen, H. / Su, N. / Wu, A. / Russell, D. / Pollard, H. / Lee, J.W. / Peng, B. / Thakur, K. / Ye, Q. / ...Authors: Dowling, J.E. / Chuaqui, C. / Pontz, T.W. / Lyne, P.D. / Larsen, N.A. / Block, M.H. / Chen, H. / Su, N. / Wu, A. / Russell, D. / Pollard, H. / Lee, J.W. / Peng, B. / Thakur, K. / Ye, Q. / Zhang, T. / Brassil, P. / Racicot, V. / Bao, L. / Denz, C.R. / Cooke, E.
History
DepositionOct 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3573
Polymers39,8781
Non-polymers4792
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.528, 61.895, 116.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 39878.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-LNH / 3-{5-(acetylamino)-3-[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]-1H-indol-1-yl}propanoic acid


Mass: 443.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N7O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22-26% PEG 6K, 200 mM ammonium sulfate, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→29.9 Å / Num. all: 17185 / Num. obs: 17196 / % possible obs: 91.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.18 % / Net I/σ(I): 10.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.47 % / Mean I/σ(I) obs: 3.4 / % possible all: 59.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.5.0046refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.01 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.01 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: THIS DATA WAS FROM A RECYCLED CRYSTAL
RfactorNum. reflection% reflectionSelection details
Rfree0.26919 892 5.2 %RANDOM
Rwork0.22094 ---
obs0.22346 16293 91.58 %-
all-17185 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.157 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.63 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 34 138 2934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022874
X-RAY DIFFRACTIONr_bond_other_d0.0010.021979
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.963892
X-RAY DIFFRACTIONr_angle_other_deg0.98934769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3475326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25623.05154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71815501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9011525
X-RAY DIFFRACTIONr_chiral_restr0.1040.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 43 -
Rwork0.239 756 -
obs--57.73 %
Refinement TLS params.Method: refined / Origin x: 16.5464 Å / Origin y: 21.7148 Å / Origin z: 19.3195 Å
111213212223313233
T0.0072 Å20.0026 Å20.0023 Å2-0.0057 Å2-0.0028 Å2--0.0202 Å2
L0.229 °2-0.0488 °2-0.1984 °2-0.6575 °20.1647 °2--0.6203 °2
S0.0385 Å °0.0085 Å °-0.0008 Å °0.0001 Å °-0.0173 Å °0.0206 Å °-0.0187 Å °0.0281 Å °-0.0211 Å °

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