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Yorodumi- PDB-3k1x: Acidic Fibroblast Growth Factor (FGF-1) complexed with dobesilate -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k1x | ||||||
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Title | Acidic Fibroblast Growth Factor (FGF-1) complexed with dobesilate | ||||||
Components | Heparin-binding growth factor 1 | ||||||
Keywords | HORMONE / acidic fibroblast growth factor / inhibitors / ACETYLATION | ||||||
Function / homology | Function and homology information mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of hepatocyte proliferation / S100 protein binding / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / fibroblast growth factor receptor signaling pathway / anatomical structure morphogenesis / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / Hsp70 protein binding / Signaling by FGFR1 in disease / activation of protein kinase B activity / positive regulation of endothelial cell migration / extracellular matrix / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / animal organ morphogenesis / Negative regulation of FGFR1 signaling / growth factor activity / positive regulation of MAP kinase activity / lung development / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / heparin binding / cellular response to heat / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Romero, A. / Fernandez, I.S. / Gimenez-Gallego, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Gentisic acid, a compound associated with plant defense and a metabolite of aspirin, heads a new class of in vivo fibroblast growth factor inhibitors. Authors: Fernandez, I.S. / Cuevas, P. / Angulo, J. / Lopez-Navajas, P. / Canales-Mayordomo, A. / Gonzalez-Corrochano, R. / Lozano, R.M. / Valverde, S. / Jimenez-Barbero, J. / Romero, A. / Gimenez-Gallego, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k1x.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k1x.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 3k1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k1x_validation.pdf.gz | 495.9 KB | Display | wwPDB validaton report |
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Full document | 3k1x_full_validation.pdf.gz | 526.4 KB | Display | |
Data in XML | 3k1x_validation.xml.gz | 34 KB | Display | |
Data in CIF | 3k1x_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/3k1x ftp://data.pdbj.org/pub/pdb/validation_reports/k1/3k1x | HTTPS FTP |
-Related structure data
Related structure data | 3jutC 1axmS 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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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 14752.703 Da / Num. of mol.: 6 / Fragment: Heparin-binding, UNP residues 24-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRAT / Production host: Escherichia coli (E. coli) / References: UniProt: P05230 #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: 2.44 Å3/Da / Density % sol: 49.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: Crystals of thecomplex between FGF-1 and 2,5-DHPS (2,5-dihydroxyphenylsulfonate) were grown using the sitting drop vapour method at 295 K. Equal volumes of protein and inhibitor solutions, 0. ...Details: Crystals of thecomplex between FGF-1 and 2,5-DHPS (2,5-dihydroxyphenylsulfonate) were grown using the sitting drop vapour method at 295 K. Equal volumes of protein and inhibitor solutions, 0.75 and 1.5mM, respectively were mixed with drops containing 60% sodium/potassium tartrate buffered with 5mM sodium phosphate [pH 7.8]. The drops were equilibrated against 0.2ml of 1.3M Li2SO4 and typical crystals grew within two weeks with approximate dimensions of 0.7 x 0.5 x 0.2 mm. , VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 7, 2008 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→94.07 Å / Num. all: 59910 / Num. obs: 59016 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 29.604 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4.5 / Num. unique all: 8011 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AXM Resolution: 1.98→24.48 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.774 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.077 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→24.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.981→2.032 Å / Total num. of bins used: 20
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