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Yorodumi- PDB-1wun: Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wun | ||||||
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Title | Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-Trp-Gln-p-aminobenzamidine | ||||||
Components |
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Keywords | HYDROLASE/BLOOD CLOTTING / SERINE PROTEASE / HYDROLASE-BLOOD CLOTTING COMPLEX | ||||||
Function / homology | Function and homology information activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / 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 ...activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / 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 / NGF-stimulated transcription / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / cytokine receptor activity / 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 / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of interleukin-8 production / protein processing / phospholipid binding / cytokine-mediated signaling pathway / Golgi lumen / circadian rhythm / response to estrogen / positive regulation of angiogenesis / activation of cysteine-type endopeptidase activity involved in apoptotic process / blood coagulation / response to estradiol / collagen-containing extracellular matrix / protease binding / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of gene expression / cell surface / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Kadono, S. / Sakamoto, A. / Kikuchi, Y. / Oh-eda, M. / Yabuta, N. / Yoshihashi, K. / Kitazawa, T. / Suzuki, T. / Koga, T. / Hattori, K. ...Kadono, S. / Sakamoto, A. / Kikuchi, Y. / Oh-eda, M. / Yabuta, N. / Yoshihashi, K. / Kitazawa, T. / Suzuki, T. / Koga, T. / Hattori, K. / Shiraishi, T. / Haramura, M. / Kodama, H. / Ono, Y. / Esaki, T. / Sato, H. / Watanabe, Y. / Itoh, S. / Ohta, M. / Kozono, T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2005 Title: Structure-based design of P3 moieties in the peptide mimetic factor VIIa inhibitor Authors: Kadono, S. / Sakamoto, A. / Kikuchi, Y. / Oh-eda, M. / Yabuta, N. / Yoshihashi, K. / Kitazawa, T. / Suzuki, T. / Koga, T. / Hattori, K. / Shiraishi, T. / Haramura, M. / Kodama, H. / Ono, Y. ...Authors: Kadono, S. / Sakamoto, A. / Kikuchi, Y. / Oh-eda, M. / Yabuta, N. / Yoshihashi, K. / Kitazawa, T. / Suzuki, T. / Koga, T. / Hattori, K. / Shiraishi, T. / Haramura, M. / Kodama, H. / Ono, Y. / Esaki, T. / Sato, H. / Watanabe, Y. / Itoh, S. / Ohta, M. / Kozono, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wun.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wun.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 1wun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wun_validation.pdf.gz | 861.4 KB | Display | wwPDB validaton report |
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Full document | 1wun_full_validation.pdf.gz | 870.7 KB | Display | |
Data in XML | 1wun_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 1wun_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/1wun ftp://data.pdbj.org/pub/pdb/validation_reports/wu/1wun | HTTPS FTP |
-Related structure data
Related structure data | 1wv7C 1danS 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
-Coagulation factor ... , 2 types, 2 molecules LH
#1: Protein | Mass: 17487.076 Da / Num. of mol.: 1 / Fragment: Factor VII light chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): CHO / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: Factor VII heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): CHO / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa |
-Protein , 1 types, 1 molecules T
#3: Protein | Mass: 24697.398 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-218 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109 / References: UniProt: P13726 |
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-Sugars , 2 types, 2 molecules
#4: Sugar | ChemComp-BGC / |
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#5: Sugar | ChemComp-FUC / |
-Non-polymers , 3 types, 367 molecules
#6: Chemical | ChemComp-CA / #7: Chemical | ChemComp-P5B / | #8: 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: 2.63 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 5000, sodium chloride, cacodylate, calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 25, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 37641 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.227 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1DAN Resolution: 2.4→19.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2101500.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: BABINET / Bsol: 280 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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