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Yorodumi- PDB-2fgi: CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF FGF RECEPTOR 1... -
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-Basic information
Entry | Database: PDB / ID: 2fgi | ||||||
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Title | CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF FGF RECEPTOR 1 IN COMPLEX WITH INHIBITOR PD173074 | ||||||
Components | PROTEIN (FIBROBLAST GROWTH FACTOR (FGF) RECEPTOR 1) | ||||||
Keywords | TRANSFERASE / PROTEIN KINASE / TYROSINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / INHIBITOR | ||||||
Function / homology | Function and homology information Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / Signaling by plasma membrane FGFR1 fusions / ventricular zone neuroblast division / diphosphate metabolic process / vitamin D3 metabolic process / regulation of phosphate transport ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / Signaling by plasma membrane FGFR1 fusions / ventricular zone neuroblast division / diphosphate metabolic process / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / FGFR1c and Klotho ligand binding and activation / cementum mineralization / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / response to sodium phosphate / receptor-receptor interaction / auditory receptor cell development / Epithelial-Mesenchymal Transition (EMT) during gastrulation / chordate embryonic development / fibroblast growth factor receptor activity / positive regulation of parathyroid hormone secretion / branching involved in salivary gland morphogenesis / positive regulation of phospholipase activity / mesenchymal cell proliferation / paraxial mesoderm development / lung-associated mesenchyme development / FGFR1b ligand binding and activation / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / cell projection assembly / cellular response to fibroblast growth factor stimulus / skeletal system morphogenesis / outer ear morphogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / middle ear morphogenesis / embryonic limb morphogenesis / inner ear morphogenesis / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / midbrain development / cardiac muscle cell proliferation / fibroblast growth factor binding / regulation of cell differentiation / positive regulation of stem cell proliferation / PI-3K cascade:FGFR1 / Formation of paraxial mesoderm / phosphatidylinositol-mediated signaling / PI3K Cascade / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / cell maturation / FRS-mediated FGFR1 signaling / positive regulation of neuron differentiation / Signaling by FGFR1 in disease / SH2 domain binding / NCAM signaling for neurite out-growth / stem cell proliferation / skeletal system development / Signal transduction by L1 / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / positive regulation of MAP kinase activity / neuron migration / receptor protein-tyrosine kinase / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / neuron projection development / cell migration / PIP3 activates AKT signaling / heparin binding / gene expression / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / cytoplasmic vesicle / protein tyrosine kinase activity / angiogenesis / in utero embryonic development / protein autophosphorylation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein phosphorylation / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Mohammadi, M. / Froum, S. / Hamby, J.M. / Schroeder, M. / Panek, R.L. / Lu, G.H. / Eliseenkova, A.V. / Green, D. / Schlessinger, J. / Hubbard, S.R. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: Crystal structure of an angiogenesis inhibitor bound to the FGF receptor tyrosine kinase domain. Authors: Mohammadi, M. / Froum, S. / Hamby, J.M. / Schroeder, M.C. / Panek, R.L. / Lu, G.H. / Eliseenkova, A.V. / Green, D. / Schlessinger, J. / Hubbard, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fgi.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fgi.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 2fgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fgi_validation.pdf.gz | 854 KB | Display | wwPDB validaton report |
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Full document | 2fgi_full_validation.pdf.gz | 868.1 KB | Display | |
Data in XML | 2fgi_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 2fgi_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/2fgi ftp://data.pdbj.org/pub/pdb/validation_reports/fg/2fgi | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9944, -0.09773, 0.04029), Vector: |
-Components
#1: Protein | Mass: 35308.613 Da / Num. of mol.: 2 / Fragment: TYROSINE KINASE DOMAIN / Mutation: L457V, C488A, C584S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Cellular location: CYTOPLASM / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11362, EC: 2.7.1.112 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 16% PEG 10000, 0.3 M (NH4)2SO4, 100 MM BIS-TRIS, PH 6.5, 5% ETHYLENE GLYCOL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Mohammadi, M., (1996) Cell, 86, 577. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 27, 1997 / Details: YALE MIRRORS |
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→30 Å / Num. obs: 24664 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.4 |
Reflection | *PLUS Num. measured all: 93535 |
Reflection shell | *PLUS % possible obs: 95.5 % / Rmerge(I) obs: 0.252 |
-Processing
Software |
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Refinement | Resolution: 2.5→6 Å / Rfactor Rfree error: 0.0081 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 45.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.816 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / σ(F): 2 / % reflection Rfree: 4.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 45.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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