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Open data
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Basic information
Entry | Database: PDB / ID: 1w0y | ||||||
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Title | tf7a_3771 complex | ||||||
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![]() | HYDROLASE / SERINE PROTEASE / BLOOD COAGULATION / GLYCOPROTEIN / PLASMA / VITAMIN K / CALCIUM-BINDING / GAMMA-CARBOXYGLUTAMIC ACID / CO-FACTOR / COAGULATION / ENZYME COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Banner, D.W. / D'Arcy, A. / Groebke-Zbinden, K. / Ackermann, J. / Kirchhofer, D. / Ji, Y.-H. / Tschopp, T.B. / Wallbaum, S. / Weber, L. | ||||||
![]() | ![]() Title: Design of Selective Phenylglycine Amide Tissue Factor/Factor Viia Inhibitors Authors: Groebke-Zbinden, K. / Banner, D.W. / Ackermann, J. / D'Arcy, A. / Kirchhofer, D. / Ji, Y.-H. / Tschopp, T.B. / Wallbaum, S. / Weber, L. #1: ![]() Title: The Crystal Structure of the Complex of Blood Coagulation Factor Viia with Soluble Tissue Factor Authors: Banner, D.W. / D'Arcy, A. / Chene, C. / Winkler, F.K. / Guha, A. / Konigsberg, W.H. / Nemerson, Y. / Kirchhofer, D. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA HB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA HB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.4 KB | Display | ![]() |
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PDB format | ![]() | 111.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 835.8 KB | Display | ![]() |
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Full document | ![]() | 848.7 KB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 42 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w2kC ![]() 1danS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | THIS DESIGNATION IS BASED ON AN AUTOMATIC QUATERNARYSTRUCTURE DETERMINATION (PQS.EBI.AC.UK). |
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Components
-BLOOD COAGULATION FACTOR ... , 2 types, 2 molecules HL
#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.) ![]() Cell line (production host): BABY HAMSTER KIDNEY CELLS (BHK) Production host: ![]() ![]() |
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#2: Protein | Mass: 16315.761 Da / Num. of mol.: 1 / Fragment: FACTOR VII HEAVY CHAIN, RESIDUES 61-202 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cell line (production host): BABY HAMSTER KIDNEY CELLS (BHK) Production host: ![]() ![]() |
-Protein , 1 types, 1 molecules T
#3: Protein | Mass: 23763.393 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 38-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/FUC.gif)
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#7: Sugar | ChemComp-FUC / |
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#8: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 384 molecules ![](data/chem/img/771.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-771 / | ||||
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#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-CAC / | #9: Water | ChemComp-HOH / | |
-Details
Compound details | THE PEPTIDE GROUP LINKING RESIDUES 192 AND 193 OF THE HEAVY CHAIN OF FACTOR VIIA IS FLIPPED 180 ...THE PEPTIDE GROUP LINKING RESIDUES 192 AND 193 OF THE HEAVY CHAIN OF FACTOR VIIA IS FLIPPED 180 DEGREES FROM THE STANDARD ACTIVE CONFORMATI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 49.5 % / Description: 1DAN WAS ROOM TEMPERATURE - THIS IS FROZEN |
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Crystal grow | pH: 5.5 / Details: pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 30, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→25 Å / Num. obs: 85076 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 3.27 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.13 |
Reflection shell | Resolution: 2.46→2.58 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.39 / % possible all: 50.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DAN Resolution: 2.5→19.99 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.3164 Å2 / ksol: 0.340884 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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