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Yorodumi- PDB-1cvw: Crystal structure of active site-inhibited human coagulation fact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cvw | ||||||
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Title | Crystal structure of active site-inhibited human coagulation factor VIIA (DES-GLA) | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / BLOOD COAGULATION / FACTOR VIIA / SERINE PROTEASE / EGF / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / positive regulation of leukocyte chemotaxis / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / 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 / circadian rhythm / protein processing / Golgi lumen / 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 | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.28 Å | ||||||
Authors | Kemball-Cook, G. / Johnson, D.J.D. / Tuddenham, E.G.D. / Harlos, K. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 1999 Title: Crystal structure of active site-inhibited human coagulation factor VIIa (des-Gla). Authors: Kemball-Cook, G. / Johnson, D.J. / Tuddenham, E.G. / Harlos, K. #1: Journal: J.Struct.Biol. / Year: 1999 Title: Crystallization and Preliminary X-ray Analysis of Active Site-Inhibited Human Coagulation Factor VIIa (des-Gla) Authors: Johnson, D.J. / Nugent, P.G. / Tuddenham, E.G. / Harlos, K. / Kemball-Cook, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cvw.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cvw.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cvw_validation.pdf.gz | 788.6 KB | Display | wwPDB validaton report |
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Full document | 1cvw_full_validation.pdf.gz | 793.7 KB | Display | |
Data in XML | 1cvw_validation.xml.gz | 16 KB | Display | |
Data in CIF | 1cvw_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/1cvw ftp://data.pdbj.org/pub/pdb/validation_reports/cv/1cvw | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6030.827 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ (production host): OVARY / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 28103.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ (production host): OVARY / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa |
#3: Chemical | ChemComp-0GE / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Compound details | THE CHLOROMETHYLKETONE GROUP AND THE ADJACENT RESIDUE OF THE INHIBITOR BIND WITH PROTEIN BY TWO ...THE CHLOROMETH |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: SOLUTION 30, HAMPTON SCREEN II, SEE REFERENCE 1, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal grow | *PLUS Details: used micro bridge |
Components of the solutions | *PLUS Conc.: 10 mg/ml / Common name: protein |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→90 Å / Num. all: 23231 / Num. obs: 22596 / % possible obs: 92.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.294 / % possible all: 72.8 |
Reflection | *PLUS Num. measured all: 345306 |
-Processing
Software |
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Refinement | Resolution: 2.28→30 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.28→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |