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Yorodumi- PDB-2dq7: Crystal Structure of Fyn kinase domain complexed with staurosporine -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dq7 | ||||||
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Title | Crystal Structure of Fyn kinase domain complexed with staurosporine | ||||||
Components | Proto-oncogene tyrosine-protein kinase Fyn | ||||||
Keywords | TRANSFERASE / Src family / kinase domain / staurosporine | ||||||
Function / homology | Function and homology information response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / growth factor receptor binding / regulation of glutamate receptor signaling pathway ...response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / growth factor receptor binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Platelet Adhesion to exposed collagen / CD28 co-stimulation / G protein-coupled glutamate receptor signaling pathway / positive regulation of protein localization to membrane / activated T cell proliferation / CRMPs in Sema3A signaling / positive regulation of cysteine-type endopeptidase activity / FLT3 signaling through SRC family kinases / negative regulation of dendritic spine maintenance / feeding behavior / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / Nephrin family interactions / DCC mediated attractive signaling / EPH-Ephrin signaling / dendrite morphogenesis / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / tau-protein kinase activity / CTLA4 inhibitory signaling / phospholipase activator activity / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / glial cell projection / Sema3A PAK dependent Axon repulsion / FCGR activation / cellular response to glycine / alpha-tubulin binding / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / forebrain development / Signaling by ERBB2 / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / FCGR3A-mediated IL10 synthesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / learning / axon guidance / actin filament / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / modulation of chemical synaptic transmission / tau protein binding / protein catabolic process / Signaling by SCF-KIT / Schaffer collateral - CA1 synapse / negative regulation of protein catabolic process / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / cellular response to hydrogen peroxide / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Aberrant PI3K in Cancer / disordered domain specific binding / calcium ion transport / DAP12 signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kinoshita, T. / Tada, T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2006 Title: Structure of human Fyn kinase domain complexed with staurosporine. Authors: Kinoshita, T. / Matsubara, M. / Ishiguro, H. / Okita, K. / Tada, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dq7.cif.gz | 71.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dq7.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/2dq7 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/2dq7 | HTTPS FTP |
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-Related structure data
Related structure data | 1qpcS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32645.377 Da / Num. of mol.: 1 / Fragment: Fyn, Protein kinase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastBac1 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P06241, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-STU / |
#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: 2.62 Å3/Da / Density % sol: 52.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.15M ammonium sulfate, 0.2M NaCl, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 19, 2006 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 9290 / Num. obs: 9281 / % possible obs: 99.9 % / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QPC Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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