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Yorodumi- PDB-1f7e: THE FIRST EGF-LIKE DOMAIN FROM HUMAN BLOOD COAGULATION FVII, NMR,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f7e | ||||||
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Title | THE FIRST EGF-LIKE DOMAIN FROM HUMAN BLOOD COAGULATION FVII, NMR, 20 STRUCTURES | ||||||
Components | PROTEIN (Blood Coagulation Factor VII) | ||||||
Keywords | BLOOD CLOTTING / FACTOR VII / BLOOD COAGULATION / EGF-LIKE DOMAIN | ||||||
Function / homology | Function and homology information coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / protein processing / Golgi lumen / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / HYBRID DISTANCE GEOMETRY - SIMULATED ANNEALING | ||||||
Authors | Kao, Y.-H. / Lee, G.F. / Wang, Y. / Starovasnik, M.A. / Kelley, R.F. / Spellman, M.W. / Lerner, L. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: The effect of O-fucosylation on the first EGF-like domain from human blood coagulation factor VII. Authors: Kao, Y.H. / Lee, G.F. / Wang, Y. / Starovasnik, M.A. / Kelley, R.F. / Spellman, M.W. / Lerner, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f7e.cif.gz | 250.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f7e.ent.gz | 206.5 KB | Display | PDB format |
PDBx/mmJSON format | 1f7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f7e_validation.pdf.gz | 342.1 KB | Display | wwPDB validaton report |
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Full document | 1f7e_full_validation.pdf.gz | 444.5 KB | Display | |
Data in XML | 1f7e_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1f7e_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/1f7e ftp://data.pdbj.org/pub/pdb/validation_reports/f7/1f7e | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4878.247 Da / Num. of mol.: 1 / Fragment: FIRST EGF-LIKE DOMAIN (RESIDUES 45-87) Source method: isolated from a genetically manipulated source Details: CALCIUM BOUND FORM / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08709 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: DETAILS ARE INCLUDED IN THE PUBLICATION. |
-Sample preparation
Sample conditions | Ionic strength: 400mM / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian INOVA 500 / Manufacturer: Varian / Model: INOVA 500 / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: HYBRID DISTANCE GEOMETRY - SIMULATED ANNEALING / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. | ||||||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION AND LOWEST XPLOR ENERGY Conformers calculated total number: 100 / Conformers submitted total number: 20 |