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Yorodumi- PDB-4g17: Crystal structure of ck1g3 with 2-[(4-TERT-BUTYLPHENYL)AMINO]-1H-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g17 | ||||||
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Title | Crystal structure of ck1g3 with 2-[(4-TERT-BUTYLPHENYL)AMINO]-1H-BENZIMIDAZOLE-6-CARBONITRILE | ||||||
Components | Casein kinase I isoform gamma-3 | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / ck1g / kinase / inhibitor / TRANSFERASE-TRANSFERASE inhibitor complex | ||||||
Function / homology | Function and homology information protein modification process / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction ...protein modification process / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Huang, X. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2012 Title: 2-Phenylamino-6-cyano-1H-benzimidazole-based isoform selective casein kinase 1 gamma (CK1g)inhibitors Authors: Hua, Z. / Huang, X. / Bregman, H. / Chakka, N. / DiMauro, E.F. / Doherty, E.M. / Goldstein, J. / Gunaydin, H. / Huang, H. / Mercede, S. / Newcomb, J. / Patel, V.F. / Turci, S.M. / Yan, J. / ...Authors: Hua, Z. / Huang, X. / Bregman, H. / Chakka, N. / DiMauro, E.F. / Doherty, E.M. / Goldstein, J. / Gunaydin, H. / Huang, H. / Mercede, S. / Newcomb, J. / Patel, V.F. / Turci, S.M. / Yan, J. / Wilson, C. / Martin, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g17.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g17.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 4g17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/4g17 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/4g17 | HTTPS FTP |
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-Related structure data
Related structure data | 4g16C 2izrS 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: 38469.223 Da / Num. of mol.: 1 / Fragment: unp residues 34-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1G3 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y6M4, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-0VN / |
#3: 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: 2.78 Å3/Da / Density % sol: 55.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100 mM Tris, 0.2 M MgCl2, 2.5-15% PEG10K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 27631 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.102 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.603 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IZR Resolution: 2.1→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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