+Open data
-Basic information
Entry | Database: PDB / ID: 1w8b | ||||||
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Title | Factor7 - 413 complex | ||||||
Components | (BLOOD COAGULATION FACTOR VIIA) x 2 | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / COAGULATION / ENZYME 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 / response to carbon dioxide / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K ...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 / response to carbon dioxide / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to thyroxine / positive regulation of leukocyte chemotaxis / response to growth hormone / response to cholesterol / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / animal organ regeneration / positive regulation of blood coagulation / 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 / response to estrogen / circadian rhythm / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w8b.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w8b.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 1w8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w8b_validation.pdf.gz | 750.3 KB | Display | wwPDB validaton report |
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Full document | 1w8b_full_validation.pdf.gz | 751.3 KB | Display | |
Data in XML | 1w8b_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1w8b_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/1w8b ftp://data.pdbj.org/pub/pdb/validation_reports/w8/1w8b | HTTPS FTP |
-Related structure data
Related structure data | 1w7xC 1w0yS S: Starting model for refinement C: citing same article (ref.) |
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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: 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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08709, coagulation factor VIIa |
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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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08709, coagulation factor VIIa |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-413 / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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Refine LS restraints |
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