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Open data
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Basic information
Entry | Database: PDB / ID: 1w8b | ||||||
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Title | Factor7 - 413 complex | ||||||
![]() | (BLOOD COAGULATION FACTOR VIIA) x 2 | ||||||
![]() | HYDROLASE / SERINE PROTEASE / COAGULATION / ENZYME COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ackermann, J. / Alig, L. / Banner, D.W. / Boehm, H.-J. / Groebke-Zbinden, K. / Hilpert, K. / Lave, T. / Kuehne, H. / Obst-Sander, U. / Riederer, M.A. ...Ackermann, J. / Alig, L. / Banner, D.W. / Boehm, H.-J. / Groebke-Zbinden, K. / Hilpert, K. / Lave, T. / Kuehne, H. / Obst-Sander, U. / Riederer, M.A. / Stahl, M. / Tschopp, T.B. / Weber, L. / Wessel, H.P. | ||||||
![]() | ![]() Title: Selective and Orally Bioavailable Phenylglycine Tissue Factor/Factor Viia Inhibitors Authors: Groebke-Zbinden, K. / Obst-Sander, U. / Hilpert, K. / Kuehne, H. / Banner, D.W. / Boehm, H.-J. / Stahl, M. / Ackermann, J. / Alig, L. / Weber, L. / Wessel, H.P. / Riederer, M.A. / Tschopp, T.B. / Lave, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.4 KB | Display | ![]() |
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PDB format | ![]() | 56.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 750.3 KB | Display | ![]() |
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Full document | ![]() | 751.3 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w7xC ![]() 1w0yS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: FACTOR VII HEAVY CHAIN, RESIDUES 213-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 6272.113 Da / Num. of mol.: 1 / Fragment: FACTOR VII LIGHT CHAIN, RESIDUES 148-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-413 / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65 % Description: ONLY 27DEGREES OF DATA WERE COLLECTED, SO COMPLETENESS IS VERY POOR. ALSO THERE WAS SEVERE ICING. |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→20 Å / Num. obs: 23089 / % possible obs: 75 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.82→2.92 Å / % possible all: 62 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1W0Y Resolution: 3→72.36 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.843 / SU B: 14.796 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R Free: 0.503 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENZYME-INHIBITOR COMPLEX WAS RECENTLY REDETERMINED AT HIGH RESOLUTION IN A DIFFERENT SPACE GROUP (1W7X.PDB). THIS ORIGINAL STRUCTURE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENZYME-INHIBITOR COMPLEX WAS RECENTLY REDETERMINED AT HIGH RESOLUTION IN A DIFFERENT SPACE GROUP (1W7X.PDB). THIS ORIGINAL STRUCTURE IS AT LOW RESOLUTION AND THE DATA IS INCOMPLETE. NEVERTHELESS THE INHIBITOR BIND MODE IS WELL DETERMINED. CURIOUSLY ONE INHIBITOR SUBSTITUENT IN THIS STRUCTURE IS DISPLACED FROM ITS POSITION SEEN IN RELATED STRUCTURES, AND RESIDUES FROM THE NEXT MOLECULE IN THE CRYSTAL FILL THE BINDING POCKET. THE LOOP 140-150 IS NOT SEEN, AND POSSIBLY SUFFERED PROTEOLYSIS.
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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: 19.41 Å2
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Refinement step | Cycle: LAST / Resolution: 3→72.36 Å
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