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Yorodumi- PDB-3pe2: Crystal structure of human protein kinase CK2 in complex with the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pe2 | ||||||
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Title | Crystal structure of human protein kinase CK2 in complex with the inhibitor CX-5011 | ||||||
Components | Casein kinase II subunit alpha | ||||||
Keywords | transferase/transferase inhibitor / Kinase / CK2-inhibitor complex / 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 / Maturation of hRSV A proteins ...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 / Maturation of hRSV A proteins / 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 / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / kinase activity / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / negative regulation of translation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / apoptotic process / 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: 1.9 Å | ||||||
Authors | Battistutta, R. / Papinutto, E. / Lolli, G. / Pierre, F. / Haddach, M. / Ryckman, D.M. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Unprecedented selectivity and structural determinants of a new class of protein kinase CK2 inhibitors in clinical trials for the treatment of cancer. Authors: Battistutta, R. / Cozza, G. / Pierre, F. / Papinutto, E. / Lolli, G. / Sarno, S. / O'Brien, S.E. / Siddiqui-Jain, A. / Haddach, M. / Anderes, K. / Ryckman, D.M. / Meggio, F. / Pinna, L.A. #1: Journal: Biochem.J. / Year: 2009 Title: Quinalizarin as a potent, selective and cell-permeable inhibitor of protein kinase CK2. Authors: Cozza, G. / Mazzorana, M. / Papinutto, E. / Bain, J. / Elliott, M. / di Maira, G. / Gianoncelli, A. / Pagano, M.A. / Sarno, S. / Ruzzene, M. / Battistutta, R. / Meggio, F. / Moro, S. / Zagotto, G. / Pinna, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pe2.cif.gz | 155.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pe2.ent.gz | 122.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pe2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/3pe2 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/3pe2 | HTTPS FTP |
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-Related structure data
Related structure data | 3pe1C 3r0tC 2pvrS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 40240.902 Da / Num. of mol.: 1 / Fragment: unp residues 1-337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) References: UniProt: P68400, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-E1B / | ||
#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: 1.99 Å3/Da / Density % sol: 38.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 32% PEG 4000, 0.2M Li2SO4, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: PILATUS 2M / Detector: PIXEL / Date: Jul 6, 2010 / Details: Mirrors |
Radiation | Monochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.44 Å / Num. all: 25295 / Num. obs: 24941 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.62 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2 / Num. unique all: 3536 / Rsym value: 0.594 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PVR Resolution: 1.9→34.135 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8607 / SU ML: 0.24 / Isotropic thermal model: Isotropic + TLS parameters / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.577 Å2 / ksol: 0.364 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.48 Å2 / Biso mean: 24.9724 Å2 / Biso min: 9.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.135 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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Refinement TLS params. | S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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