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Yorodumi- PDB-2b8o: Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor VIIa/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b8o | ||||||
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Title | Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor VIIa/Soluble Tissue Factor Complex | ||||||
Components |
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Keywords | hydrolase/hydrolase inhibitor / Serine protease / Tissue factor / EGR / blood coagualtion / clotting / clotting factor / coagulation factor / hydrolase-hydrolase inhibitor COMPLEX | ||||||
Function / homology | Function and homology information activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / 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 plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / 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 / phospholipid binding / protein processing / 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 / external side of plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Bajaj, S.P. / Schmidt, A.E. / Padmanabhan, K. | ||||||
Citation | Journal: To be published Title: Crystal Structure of Factor VIIa/soluble Tissue Factor complexed with Glu-Gly-Arg-Chloromethyl ketone Authors: Bajaj, S.P. / Schmidt, A.E. / Padmanabhan, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b8o.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b8o.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 2b8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/2b8o ftp://data.pdbj.org/pub/pdb/validation_reports/b8/2b8o | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Coagulation factor VII ... , 2 types, 2 molecules LH
#1: Protein | Mass: 16359.772 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / References: UniProt: P08709 |
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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) / Gene: F7 / References: UniProt: P08709, coagulation factor VIIa |
-Protein , 1 types, 1 molecules T
#3: Protein | Mass: 23302.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / References: UniProt: P13726 |
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-Sugars , 2 types, 2 molecules
#4: Sugar | ChemComp-GLC / |
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#5: Sugar | ChemComp-FUC / |
-Non-polymers , 7 types, 254 molecules
#6: Chemical | ChemComp-CA / #7: Chemical | #8: Chemical | ChemComp-0GJ / | #9: Chemical | ChemComp-NA / | #10: Chemical | #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CMK-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CMK-CHLOROMETH |
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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: 2.65 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Tris, sodium chloride, calcium chloride, PEG 4000, ADA, magnesium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.725 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.725 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 20383 / Num. obs: 20351 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.17 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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