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Yorodumi- PDB-1hkn: A complex between acidic fibroblast growth factor and 5-amino-2-n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hkn | ||||||
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Title | A complex between acidic fibroblast growth factor and 5-amino-2-naphthalenesulfonate | ||||||
Components | HEPARIN-BINDING GROWTH FACTOR 1 | ||||||
Keywords | GROWTH FACTOR / MITOGEN / ANGIOGENESIS / HEPARIN-BINDING | ||||||
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: 2 Å | ||||||
Authors | Fernandez-Tornero, C. / Lozano, R.M. / Gimenez-Gallego, G. / Romero, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Leads for Development of New Naphthalenesulfonate Derivatives with Enhanced Antiangiogenic Activity: Crystal Structure of Acidic Fibroblast Growth Factor in Complex with 5-Amino-2-Naphthalenesulfonate Authors: Fernandez-Tornero, C. / Lozano, R.M. / Redondo-Horcajo, M. / Gomez, A. / Lopez, J. / Quesada, E. / Uriel, C. / Valverde, S. / Cuevas, P. / Romero, A. / Gimenez-Gallego, G. #1: Journal: J.Mol.Biol. / Year: 1998 Title: Solution Structure of Acidic Fibroblast Growth Factor Bound to 1,3,6-Naphthalenetrisulfonate: A Minimal Model for the Anti-Tumoral Action of Suramins and Suradistas Authors: Lozano, M.R. / Jimenez, M. / Santoro, J. / Rico, M. / Gimenez-Gallego, G. #2: Journal: Eur.J.Biochem. / Year: 1996 Title: X-Ray Structure of Native Full-Length Human Fibroblast-Growth Factor at 0.25 Nm Resolution Authors: Romero, A. / Pineda-Lucena, A. / Gimenez-Gallego, G. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hkn.cif.gz | 168.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hkn.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 1hkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hkn_validation.pdf.gz | 491.3 KB | Display | wwPDB validaton report |
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Full document | 1hkn_full_validation.pdf.gz | 510.8 KB | Display | |
Data in XML | 1hkn_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 1hkn_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/1hkn ftp://data.pdbj.org/pub/pdb/validation_reports/hk/1hkn | HTTPS FTP |
-Related structure data
Related structure data | 2axmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 15710.691 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / 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: 2.03 Å3/Da / Density % sol: 39.1 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: CRYSTALS OF THE COMPLEX BETWEEN AFGF AND 5-AMINO-2-NMS WERE GROWN BY MIXING 0.75 MM PROTEIN, 1.5 MM OF THE INHIBITOR AND 60% SODIUM/PO, pH 7.80 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / pH: 7.85 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9073 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2001 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9073 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.5 Å / Num. obs: 56957 / % possible obs: 99.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 3 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 2.4 / % possible all: 99 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 33.5 Å / Num. measured all: 321819 / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY: PDB ENTRY 2AXM Resolution: 2→33.57 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1758636.06 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE EXPERIMENT PHE1001-LYS1009, PHE2001-LYS2009, PHE3001-TYR3008, PHE4001-LYS4009, PHE5001-TYR5008, PHE6001- LYS6009 SEVERAL RESIDUES AT THE C- ...Details: THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE EXPERIMENT PHE1001-LYS1009, PHE2001-LYS2009, PHE3001-TYR3008, PHE4001-LYS4009, PHE5001-TYR5008, PHE6001- LYS6009 SEVERAL RESIDUES AT THE C-TERMINAL WERE NOT MODELLED SER1138-ASP1140, SER2138-ASP2140, SER3138-ASP3140, SER1139- ASP4140, SER5139-ASP5140, SER6138-ASP6140
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.5897 Å2 / ksol: 0.387043 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→33.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.231 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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