+Open data
-Basic information
Entry | Database: PDB / ID: 1j9c | ||||||
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Title | Crystal Structure of tissue factor-factor VIIa complex | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / mobile loop / BLOOD CLOTTING / Hydrolase-hydrolase inhibitor 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Huang, M. / Ruf, W. / Edgington, T.S. / Wilson, I.A. | ||||||
Citation | Journal: To be Published Title: Ligand Induced Conformational Transitions of Tissue Factor. Crystal Structure of the Tissue Factor:Factor VIIa Complex. Authors: Huang, M. / Ruf, W. / Edgington, T.S. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j9c.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j9c.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 1j9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j9c_validation.pdf.gz | 524.9 KB | Display | wwPDB validaton report |
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Full document | 1j9c_full_validation.pdf.gz | 557.7 KB | Display | |
Data in XML | 1j9c_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 1j9c_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/1j9c ftp://data.pdbj.org/pub/pdb/validation_reports/j9/1j9c | 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 TLH
#1: Protein | Mass: 23763.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P13726 |
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#2: Protein | Mass: 10371.550 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): BHK / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709 |
#3: Protein | Mass: 28103.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): BHK / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709 |
-Sugars , 3 types, 3 molecules
#4: Sugar | ChemComp-GLC / |
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#5: Sugar | ChemComp-FUL / |
#7: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 129 molecules
#6: Chemical | ChemComp-0Z6 / |
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#8: Chemical | ChemComp-CA / |
#9: Water | ChemComp-HOH / |
-Details
Nonpolymer details | THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PHE-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PHE-ARG-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: 3.29 Å3/Da / Density % sol: 62.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2% PEG 400, 2% 2-propanol, 2% PEG 4000, 12.5mM Calcium chloride, 2.0M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 177 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 4, 1999 Details: 58 cm long, Pt-coated, fused silica, vertical focusmirror |
Radiation | Monochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→99 Å / Num. obs: 18285 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: -0.6 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.369 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1dan Resolution: 2.9→53.94 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 275465.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.46 Å2 / ksol: 0.344 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→53.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
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Xplor file |
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