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Yorodumi- PDB-4ff8: Inhibitor bound structure of the kinase domain of the murine rece... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ff8 | ||||||
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Title | Inhibitor bound structure of the kinase domain of the murine receptor tyrosine kinase TYRO3 (Sky) | ||||||
Components | Tyrosine-protein kinase receptor TYRO3 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Receptor Protein Tyrosine Kinase / Phosphotransferase / Gas6 (ligand) / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information forebrain cell migration / lymphocyte activation / negative regulation of lymphocyte activation / natural killer cell differentiation / negative regulation of toll-like receptor signaling pathway / secretion by cell / positive regulation of viral life cycle / apoptotic cell clearance / ovulation cycle / vagina development ...forebrain cell migration / lymphocyte activation / negative regulation of lymphocyte activation / natural killer cell differentiation / negative regulation of toll-like receptor signaling pathway / secretion by cell / positive regulation of viral life cycle / apoptotic cell clearance / ovulation cycle / vagina development / neuropeptide signaling pathway / phosphatidylinositol 3-kinase binding / phagocytosis / negative regulation of innate immune response / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / phosphatidylinositol 3-kinase/protein kinase B signal transduction / establishment of localization in cell / neuron migration / receptor protein-tyrosine kinase / platelet aggregation / platelet activation / negative regulation of inflammatory response / neuron cellular homeostasis / cell surface receptor protein tyrosine kinase signaling pathway / cell migration / virus receptor activity / nuclear envelope / nervous system development / spermatogenesis / protein tyrosine kinase activity / neuron apoptotic process / negative regulation of neuron apoptotic process / protein autophosphorylation / receptor complex / endoplasmic reticulum membrane / cell surface / ATP binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ohren, J.F. / Powell, N.A. / Kohrt, J. / Perrin, L.A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Highly selective 2,4-diaminopyrimidine-5-carboxamide inhibitors of Sky kinase. Authors: Powell, N.A. / Hoffman, J.K. / Ciske, F.L. / Kaufman, M.D. / Kohrt, J.T. / Quin, J. / Sheehan, D.J. / Delaney, A. / Baxi, S.M. / Catana, C. / McConnell, P. / Ohren, J. / Perrin, L.A. / Edmunds, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ff8.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ff8.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ff8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/4ff8 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/4ff8 | 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: 36771.449 Da / Num. of mol.: 1 / Mutation: kinase domain (UNP Residues 485-800) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tyro3, Dtk, Rse / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P55144, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-14S / |
#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: 2.23 Å3/Da / Density % sol: 44.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 17% PEG 3350, 0.1M magnesium nitrate, 0.1 M Bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 25, 2005 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. all: 15860 / Num. obs: 13687 / % possible obs: 86.3 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 |
Reflection shell | Resolution: 2.24→2.32 Å / % possible all: 26.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.67 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.861 / SU B: 7.735 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.275 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.809 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→47.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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