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Yorodumi- PDB-7uy3: Crystal structure of human Fgr tyrosine kinase in complex with TL02-59 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uy3 | ||||||
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Title | Crystal structure of human Fgr tyrosine kinase in complex with TL02-59 | ||||||
Components | Tyrosine-protein kinase Fgr | ||||||
Keywords | TRANSFERASE / Fgr / TL02-59 / SIGNALING PROTEIN / kinase | ||||||
Function / homology | Function and homology information immune response-regulating cell surface receptor signaling pathway / negative regulation of natural killer cell activation / positive regulation of mast cell degranulation / Fc-gamma receptor I complex binding / regulation of phagocytosis / regulation of protein kinase activity / aggresome / myoblast proliferation / skeletal system morphogenesis / Platelet sensitization by LDL ...immune response-regulating cell surface receptor signaling pathway / negative regulation of natural killer cell activation / positive regulation of mast cell degranulation / Fc-gamma receptor I complex binding / regulation of phagocytosis / regulation of protein kinase activity / aggresome / myoblast proliferation / skeletal system morphogenesis / Platelet sensitization by LDL / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of innate immune response / bone mineralization / FCGR activation / immunoglobulin receptor binding / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of inflammatory response to antigenic stimulus / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / positive regulation of cytokine production / integrin-mediated signaling pathway / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / response to virus / mitochondrial intermembrane space / ruffle membrane / peptidyl-tyrosine phosphorylation / actin cytoskeleton / regulation of cell shape / protein tyrosine kinase activity / secretory granule lumen / protein autophosphorylation / mitochondrial inner membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / defense response to Gram-positive bacterium / positive regulation of cell migration / protein phosphorylation / innate immune response / signaling receptor binding / Neutrophil degranulation / protein kinase binding / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Du, S. / Alvarado, J.J. / Smithgall, T.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2022 Title: ATP-site inhibitors induce unique conformations of the acute myeloid leukemia-associated Src-family kinase, Fgr. Authors: Du, S. / Alvarado, J.J. / Wales, T.E. / Moroco, J.A. / Engen, J.R. / Smithgall, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uy3.cif.gz | 178.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uy3.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 7uy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/7uy3 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/7uy3 | HTTPS FTP |
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-Related structure data
Related structure data | 7uy0C 2srcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52241.254 Da / Num. of mol.: 1 / Mutation: Q528E, P529E, G530I, D531P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGR, SRC2 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P09769, non-specific protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-OJL / | ||
#3: Chemical | ChemComp-EDO / | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: For co-crystallization with TL02-59, Fgr (3.2 mg/mL in 20 mM Tris-HCl, pH 8.3, 100 mM NaCl, and 2 mM TCEP) was mixed with 10 mM TL02-59 (in 100% DMSO) to a final concentration of 120 microM ...Details: For co-crystallization with TL02-59, Fgr (3.2 mg/mL in 20 mM Tris-HCl, pH 8.3, 100 mM NaCl, and 2 mM TCEP) was mixed with 10 mM TL02-59 (in 100% DMSO) to a final concentration of 120 microM (0.6% DMSO final) and incubated for thirty minutes at 298 K. Diffraction quality crystals were grown by sitting- and hanging-drop vapor diffusion at 277 K by mixing Fgr/TL02-59 in a 1:1 ratio with the mother liquor (0.1 M HEPES, pH 7.5, 0.8 M sodium phosphate, 0.8 M potassium phosphate and 1% 1,2-butanediol) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9757 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9757 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.99→46.233 Å / Num. obs: 33705 / % possible obs: 99.9 % / Redundancy: 10.954 % / Biso Wilson estimate: 84.007 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.131 / Χ2: 0.905 / Net I/σ(I): 11.89 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2SRC Resolution: 2.99→46.233 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 232.45 Å2 / Biso mean: 104.6638 Å2 / Biso min: 53.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.99→46.233 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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