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Yorodumi- PDB-5n1v: Crystal structure of the protein kinase CK2 catalytic subunit in ... -
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-Basic information
Entry | Database: PDB / ID: 5n1v | ||||||
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Title | Crystal structure of the protein kinase CK2 catalytic subunit in complex with pyrazolo-pyrimidine macrocyclic ligand | ||||||
Components | Casein kinase II subunit alphaCasein kinase 2 | ||||||
Keywords | TRANSFERASE / KINASE | ||||||
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 / Maturation of hRSV A proteins / Receptor Mediated Mitophagy / Sin3-type complex / Synthesis of PC ...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 / Maturation of hRSV A proteins / 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 / negative regulation of double-strand break repair via homologous recombination / chaperone-mediated protein folding / negative regulation of ubiquitin-dependent protein catabolic process / Signal transduction by L1 / peptidyl-threonine phosphorylation / Hsp90 protein binding / 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 / 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 / negative regulation of translation / protein stabilization / non-specific serine/threonine protein kinase / regulation of cell cycle / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Robb, G. / Ferguson, A. / Hargreaves, D. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors. Authors: McCoull, W. / Abrams, R.D. / Anderson, E. / Blades, K. / Barton, P. / Box, M. / Burgess, J. / Byth, K. / Cao, Q. / Chuaqui, C. / Carbajo, R.J. / Cheung, T. / Code, E. / Ferguson, A.D. / ...Authors: McCoull, W. / Abrams, R.D. / Anderson, E. / Blades, K. / Barton, P. / Box, M. / Burgess, J. / Byth, K. / Cao, Q. / Chuaqui, C. / Carbajo, R.J. / Cheung, T. / Code, E. / Ferguson, A.D. / Fillery, S. / Fuller, N.O. / Gangl, E. / Gao, N. / Grist, M. / Hargreaves, D. / Howard, M.R. / Hu, J. / Kemmitt, P.D. / Nelson, J.E. / O'Connell, N. / Prince, D.B. / Raubo, P. / Rawlins, P.B. / Robb, G.R. / Shi, J. / Waring, M.J. / Whittaker, D. / Wylot, M. / Zhu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n1v.cif.gz | 297.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n1v.ent.gz | 243 KB | Display | PDB format |
PDBx/mmJSON format | 5n1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/5n1v ftp://data.pdbj.org/pub/pdb/validation_reports/n1/5n1v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40982.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Komagataella pastoris (fungus) References: UniProt: P68400, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→128.77 Å / Num. obs: 36530 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 69.05 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.52→3.08 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→91.05 Å / Cor.coef. Fo:Fc: 0.9499 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.321 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.326 / SU Rfree Blow DPI: 0.231 / SU Rfree Cruickshank DPI: 0.233
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Displacement parameters | Biso mean: 57.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→91.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.59 Å / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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