+Open data
-Basic information
Entry | Database: PDB / ID: 3a4o | ||||||
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Title | Lyn kinase domain | ||||||
Components | Tyrosine-protein kinase Lyn | ||||||
Keywords | TRANSFERASE / Src family / kinase domain / Alternative splicing / ATP-binding / Host-virus interaction / Kinase / Lipoprotein / Myristate / Nucleotide-binding / Palmitate / Phosphoprotein / Polymorphism / Proto-oncogene / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / negative regulation of intracellular signal transduction / response to sterol depletion / regulation of mast cell activation / negative regulation of myeloid leukocyte differentiation / eosinophil differentiation / Fc receptor mediated stimulatory signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / positive regulation of dendritic cell apoptotic process ...C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / negative regulation of intracellular signal transduction / response to sterol depletion / regulation of mast cell activation / negative regulation of myeloid leukocyte differentiation / eosinophil differentiation / Fc receptor mediated stimulatory signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / positive regulation of dendritic cell apoptotic process / positive regulation of oligodendrocyte progenitor proliferation / Fc receptor mediated inhibitory signaling pathway / regulation of B cell receptor signaling pathway / tolerance induction to self antigen / integrin alpha2-beta1 complex / negative regulation of toll-like receptor 2 signaling pathway / immune response-regulating cell surface receptor signaling pathway / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of mast cell proliferation / negative regulation of mast cell proliferation / glycosphingolipid binding / negative regulation of toll-like receptor 4 signaling pathway / regulation of mast cell degranulation / platelet degranulation / phosphorylation-dependent protein binding / : / regulation of platelet aggregation / dendritic cell differentiation / regulation of B cell apoptotic process / oligodendrocyte development / phosphatidylinositol 3-kinase activator activity / Signaling by Erythropoietin / histamine secretion by mast cell / Erythropoietin activates STAT5 / interleukin-5-mediated signaling pathway / Erythropoietin activates Phospholipase C gamma (PLCG) / Platelet Adhesion to exposed collagen / CD28 co-stimulation / negative regulation of immune response / regulation of release of sequestered calcium ion into cytosol / CD22 mediated BCR regulation / gamma-tubulin binding / platelet-derived growth factor receptor binding / response to carbohydrate / Fc epsilon receptor (FCERI) signaling / EPH-Ephrin signaling / toll-like receptor 4 signaling pathway / Regulation of KIT signaling / postsynaptic specialization, intracellular component / CTLA4 inhibitory signaling / leukocyte migration / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / Dectin-2 family / negative regulation of B cell proliferation / mitochondrial crista / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / Fc-epsilon receptor signaling pathway / regulation of cell adhesion mediated by integrin / positive regulation of glial cell proliferation / B cell homeostasis / FCGR activation / EPH-ephrin mediated repulsion of cells / response to axon injury / ephrin receptor signaling pathway / fatty acid transport / response to amino acid / growth hormone receptor signaling pathway via JAK-STAT / Role of LAT2/NTAL/LAB on calcium mobilization / hematopoietic progenitor cell differentiation / regulation of ERK1 and ERK2 cascade / Erythropoietin activates RAS / Growth hormone receptor signaling / cellular response to retinoic acid / Signaling by CSF3 (G-CSF) / positive regulation of tyrosine phosphorylation of STAT protein / lipopolysaccharide-mediated signaling pathway / negative regulation of MAP kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / regulation of cytokine production / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / CD209 (DC-SIGN) signaling / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to hormone / negative regulation of protein phosphorylation / DNA damage checkpoint signaling / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / phosphoprotein binding / FCERI mediated MAPK activation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Miyano, N. / Kinoshita, T. / Tada, T. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Structural basis for the inhibitor recognition of human Lyn kinase domain Authors: Miyano, N. / Kinoshita, T. / Nakai, R. / Kirii, Y. / Yokota, 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 | 3a4o.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a4o.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 3a4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a4o_validation.pdf.gz | 851.5 KB | Display | wwPDB validaton report |
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Full document | 3a4o_full_validation.pdf.gz | 894.6 KB | Display | |
Data in XML | 3a4o_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 3a4o_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/3a4o ftp://data.pdbj.org/pub/pdb/validation_reports/a4/3a4o | HTTPS FTP |
-Related structure data
Related structure data | 2dq7S 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: 32994.816 Da / Num. of mol.: 1 / Fragment: residues in UNP 233-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P07948, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-STU / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: pH 8.5, 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: Jun 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 6212 / Num. obs: 5892 |
Reflection shell | Resolution: 3→3.14 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DQ7 Resolution: 3→50 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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