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Yorodumi- PDB-1z3u: Structure of the Angiopoietin-2 Recptor Binding Domain and Identi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z3u | ||||||
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Title | Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition | ||||||
Components | Angiopoietin-2 | ||||||
Keywords | SIGNALING PROTEIN / Tie2 binding / angiogenesis / extracellular ligand | ||||||
Function / homology | Function and homology information negative regulation of positive chemotaxis / Tie signaling pathway / glomerulus vasculature development / negative regulation of cell-substrate adhesion / negative regulation of blood vessel endothelial cell migration / germ cell development / maternal process involved in female pregnancy / animal organ regeneration / response to glucose / negative regulation of angiogenesis ...negative regulation of positive chemotaxis / Tie signaling pathway / glomerulus vasculature development / negative regulation of cell-substrate adhesion / negative regulation of blood vessel endothelial cell migration / germ cell development / maternal process involved in female pregnancy / animal organ regeneration / response to glucose / negative regulation of angiogenesis / response to mechanical stimulus / Tie2 Signaling / response to activity / cell projection / response to organic cyclic compound / receptor tyrosine kinase binding / cellular response to growth factor stimulus / positive regulation of angiogenesis / gene expression / angiogenesis / collagen-containing extracellular matrix / response to hypoxia / signaling receptor binding / signal transduction / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Barton, W.A. / Tzvetkova, D. / Nikolov, D.B. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Structure of the angiopoietin-2 receptor binding domain and identification of surfaces involved in Tie2 recognition. Authors: Barton, W.A. / Tzvetkova, D. / Nikolov, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z3u.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z3u.ent.gz | 152.7 KB | Display | PDB format |
PDBx/mmJSON format | 1z3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z3u_validation.pdf.gz | 456.1 KB | Display | wwPDB validaton report |
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Full document | 1z3u_full_validation.pdf.gz | 482.1 KB | Display | |
Data in XML | 1z3u_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 1z3u_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/1z3u ftp://data.pdbj.org/pub/pdb/validation_reports/z3/1z3u | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 24597.363 Da / Num. of mol.: 4 / Fragment: Receptor binding domain (residues 281-496) / Mutation: F469A, Y475A, Y476A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O15123 #2: Chemical | ChemComp-CA / #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: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: Ammonium Sulfate and PEG-4000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 1, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 51121 / Num. obs: 50119 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Highest resolution: 2.25 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.25→8 Å
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