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Yorodumi- PDB-3owk: Human CK2 catalytic domain in complex with a benzopyridoindole de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3owk | ||||||
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Title | Human CK2 catalytic domain in complex with a benzopyridoindole derivative inhibitor | ||||||
Components | CSNK2A1 proteinCasein kinase 2, alpha 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / SERINE/THREONINE-PROTEIN KINASE / CK2 / inhibitor / benzopyridoindole / ellipticine / Transferase / 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 / phosphorylation / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Reiser, J.-B. / Prudent, R. / Cochet, C. | ||||||
Citation | Journal: Cancer Res. / Year: 2010 Title: Antitumor activity of pyridocarbazole and benzopyridoindole derivatives that inhibit protein kinase CK2. Authors: Prudent, R. / Moucadel, V. / Nguyen, C.H. / Barette, C. / Schmidt, F. / Florent, J.C. / Lafanechere, L. / Sautel, C.F. / Duchemin-Pelletier, E. / Spreux, E. / Filhol, O. / Reiser, J.B. / Cochet, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3owk.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3owk.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 3owk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/3owk ftp://data.pdbj.org/pub/pdb/validation_reports/ow/3owk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39650.223 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-331 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5U5J2, UniProt: P68400*PLUS | ||
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#2: Chemical | ChemComp-18E / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 36% polyethylene glycol 5000 monomethyl ether, 150 mM ammonium sulfate and 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.5 Å / Num. all: 29347 / Num. obs: 29347 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 21.62 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2370 / Rsym value: 0.357 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.12 Å / Cor.coef. Fo:Fc: 0.942 / SU B: 3.072 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.841 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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