+Open data
-Basic information
Entry | Database: PDB / ID: 2zv7 | ||||||
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Title | Lyn Tyrosine Kinase Domain, apo form | ||||||
Components | Tyrosine-protein kinase Lyn | ||||||
Keywords | TRANSFERASE / Lyn Kinase / Alternative splicing / ATP-binding / Kinase / Lipoprotein / Myristate / Nucleotide-binding / Palmitate / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information Signaling by Erythropoietin / Growth hormone receptor signaling / erythropoietin receptor binding / 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 / Platelet Adhesion to exposed collagen / negative regulation of myeloid leukocyte differentiation ...Signaling by Erythropoietin / Growth hormone receptor signaling / erythropoietin receptor binding / 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 / Platelet Adhesion to exposed collagen / negative regulation of myeloid leukocyte differentiation / Fc epsilon receptor (FCERI) signaling / Dectin-2 family / PECAM1 interactions / CD22 mediated BCR regulation / CD28 co-stimulation / Signaling by CSF3 (G-CSF) / CTLA4 inhibitory signaling / Erythropoietin activates RAS / eosinophil differentiation / Regulation of KIT signaling / Fc receptor mediated stimulatory signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / EPHA-mediated growth cone collapse / 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 / EPH-ephrin mediated repulsion of cells / GPVI-mediated activation cascade / EPHB-mediated forward signaling / regulation of B cell receptor signaling pathway / FCERI mediated MAPK activation / Inactivation of CSF3 (G-CSF) signaling / tolerance induction to self antigen / integrin alpha2-beta1 complex / Signaling by SCF-KIT / negative regulation of toll-like receptor 2 signaling pathway / immune response-regulating cell surface receptor signaling pathway / FCGR activation / Cyclin D associated events in G1 / positive regulation of mast cell proliferation / negative regulation of mast cell proliferation / glycosphingolipid binding / FCERI mediated Ca+2 mobilization / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemoglobin biosynthetic process / negative regulation of toll-like receptor 4 signaling pathway / regulation of mast cell degranulation / FCERI mediated NF-kB activation / platelet degranulation / phosphorylation-dependent protein binding / Cell surface interactions at the vascular wall / : / Regulation of signaling by CBL / regulation of platelet aggregation / dendritic cell differentiation / regulation of B cell apoptotic process / CD209 (DC-SIGN) signaling / oligodendrocyte development / phosphatidylinositol 3-kinase activator activity / histamine secretion by mast cell / interleukin-5-mediated signaling pathway / regulation of release of sequestered calcium ion into cytosol / gamma-tubulin binding / platelet-derived growth factor receptor binding / response to carbohydrate / toll-like receptor 4 signaling pathway / postsynaptic specialization, intracellular component / negative regulation of B cell proliferation / mitochondrial crista / regulation of cell adhesion mediated by integrin / positive regulation of glial cell proliferation / positive regulation of phosphorylation / B cell homeostasis / hemopoiesis / response to axon injury / response to amino acid / hematopoietic progenitor cell differentiation / regulation of ERK1 and ERK2 cascade / cellular response to retinoic acid / lipopolysaccharide-mediated signaling pathway / negative regulation of MAP kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / regulation of cytokine production / ephrin receptor binding / erythrocyte differentiation / response to hormone / negative regulation of protein phosphorylation / DNA damage checkpoint signaling / phosphoprotein binding / adherens junction / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / response to insulin / regulation of erythrocyte differentiation / peptidyl-tyrosine phosphorylation / mitochondrial membrane / response to organic cyclic compound / cytoplasmic side of plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Williams, N.K. / Rossjohn, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal Structures of the Lyn Protein Tyrosine Kinase Domain in Its Apo- and Inhibitor-bound State Authors: Williams, N.K. / Lucet, I.S. / Klinken, S.P. / Ingley, E. / Rossjohn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zv7.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zv7.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zv7_validation.pdf.gz | 407.1 KB | Display | wwPDB validaton report |
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Full document | 2zv7_full_validation.pdf.gz | 409.1 KB | Display | |
Data in XML | 2zv7_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 2zv7_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/2zv7 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/2zv7 | HTTPS FTP |
-Related structure data
Related structure data | 2zv8C 2zv9C 2zvaC 1qpdS 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: 31810.639 Da / Num. of mol.: 1 / Fragment: Kinase Domain, residues 239-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 References: UniProt: P25911, non-specific protein-tyrosine kinase |
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#2: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE IS BASED ON REFERENCE 1 IN THE DATABASE, LYN_MOUSE. |
-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: 53.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 23% polyethylene glycol 3350, 0.1M NaCl, 0.1M Na-Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→63.3 Å / Num. obs: 11259 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QPD Resolution: 2.5→38.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 22.825 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.479 / ESU R Free: 0.265 / 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: 29.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→38.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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