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Yorodumi- PDB-2zzu: Human Factor VIIA-Tissue Factor Complexed with ethylsulfonamide-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zzu | ||||||
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Title | Human Factor VIIA-Tissue Factor Complexed with ethylsulfonamide-D-5-(3-carboxybenzyloxy)-Trp-Gln-p-aminobenzamidine | ||||||
Components |
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Keywords | HYDROLASE/BLOOD CLOTTING / SERINE PROTEASE / BLOOD COAGULATION / CLEAVAGE ON PAIR OF BASIC RESIDUES / DISEASE MUTATION / EGF-LIKE DOMAIN / GAMMA-CARBOXYGLUTAMIC ACID / GLYCOPROTEIN / HYDROLASE / HYDROXYLATION / PROTEASE / ZYMOGEN / LIPOPROTEIN / MEMBRANE / PALMITATE / TRANSMEMBRANE / HYDROLASE-BLOOD CLOTTING COMPLEX / SECRETED | ||||||
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: 2.5 Å | ||||||
Authors | Kadono, S. / Sakamoto, A. / Kikuchi, Y. / Oh-Eda, M. / Yabuta, N. / Koga, T. / Hattori, K. / Shiraishi, T. / Haramura, M. / Sato, H. ...Kadono, S. / Sakamoto, A. / Kikuchi, Y. / Oh-Eda, M. / Yabuta, N. / Koga, T. / Hattori, K. / Shiraishi, T. / Haramura, M. / Sato, H. / Ohta, M. / Kozono, T. | ||||||
Citation | Journal: Chem.Pharm.Bull. / Year: 2010 Title: Design and synthesis of peptidomimetic factor VIIa inhibitors Authors: Shiraishi, T. / Kadono, S. / Haramura, M. / Kodama, H. / Ono, Y. / Iikura, H. / Esaki, T. / Koga, T. / Hattori, K. / Watanabe, Y. / Sakamoto, A. / Yoshihashi, K. / Kitazawa, T. / Esaki, K. / ...Authors: Shiraishi, T. / Kadono, S. / Haramura, M. / Kodama, H. / Ono, Y. / Iikura, H. / Esaki, T. / Koga, T. / Hattori, K. / Watanabe, Y. / Sakamoto, A. / Yoshihashi, K. / Kitazawa, T. / Esaki, K. / Ohta, M. / Sato, H. / Kozono, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zzu.cif.gz | 146 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zzu.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zzu_validation.pdf.gz | 849.8 KB | Display | wwPDB validaton report |
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Full document | 2zzu_full_validation.pdf.gz | 862.2 KB | Display | |
Data in XML | 2zzu_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 2zzu_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/2zzu ftp://data.pdbj.org/pub/pdb/validation_reports/zz/2zzu | HTTPS FTP |
-Related structure data
Related structure data | 1danS S: Starting model for refinement |
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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
-Protein , 3 types, 3 molecules LHT
#1: Protein | Mass: 17487.076 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 61-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Cell (production host): CHO / 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 / Fragment: UNP RESIDUES 213-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Cell (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa |
#3: Protein | Mass: 24697.398 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM-109 / References: UniProt: P13726 |
-Sugars , 2 types, 2 molecules
#4: Sugar | ChemComp-BGC / |
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#5: Sugar | ChemComp-FUC / |
-Non-polymers , 3 types, 372 molecules
#6: Chemical | ChemComp-CA / #7: Chemical | ChemComp-359 / | #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: 2.58 Å3/Da / Density % sol: 52.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 8% PEG5000, 0.1M sodium chloride, 0.005M calcium chloride, 0.1M cacodylate, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 2, 2001 / Details: MIRRORS |
Radiation | Monochromator: CONFOCAL BLUE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 28430 / % possible obs: 97.2 % / Observed criterion σ(I): 1 / Redundancy: 3.55 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 3.95 / Num. unique all: 2729 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1DAN Resolution: 2.5→20 Å / Isotropic thermal model: isotroopic / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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