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Yorodumi- PDB-2aei: Crystal structure of a ternary complex of factor VIIa/tissue fact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aei | ||||||
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Title | Crystal structure of a ternary complex of factor VIIa/tissue factor and 2-[[6-[3-(aminoiminomethyl)phenoxy]-3,5-difluro-4-[(1-methyl-3-phenylpropyl)amino]-2-pyridinyl]oxy]-benzoic acid | ||||||
Components |
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Keywords | HYDROLASE / BLOOD COAGULATION / SERINE PROTEASE / THROMBOSIS / GLA / PYRIDINE / BENZAMIDINE / TISSUE FACTOR / COFACTOR / ENZYME 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: 2.52 Å | ||||||
Authors | Adler, M. / Whitlow, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2005 Title: The discovery of fluoropyridine-based inhibitors of the Factor VIIa/TF complex. Authors: Kohrt, J.T. / Filipski, K.J. / Cody, W.L. / Cai, C. / Dudley, D.A. / Van Huis, C.A. / Willardsen, J.A. / Rapundalo, S.T. / Saiya-Cork, K. / Leadley, R.J. / Narasimhan, L. / Zhang, E. / ...Authors: Kohrt, J.T. / Filipski, K.J. / Cody, W.L. / Cai, C. / Dudley, D.A. / Van Huis, C.A. / Willardsen, J.A. / Rapundalo, S.T. / Saiya-Cork, K. / Leadley, R.J. / Narasimhan, L. / Zhang, E. / Whitlow, M. / Adler, M. / McLean, K. / Chou, Y.L. / McKnight, C. / Arnaiz, D.O. / Shaw, K.J. / Light, D.R. / Edmunds, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aei.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aei.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 2aei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aei_validation.pdf.gz | 902.3 KB | Display | wwPDB validaton report |
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Full document | 2aei_full_validation.pdf.gz | 921.9 KB | Display | |
Data in XML | 2aei_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 2aei_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/2aei ftp://data.pdbj.org/pub/pdb/validation_reports/ae/2aei | 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
-Coagulation factor ... , 2 types, 2 molecules LH
#1: Protein | Mass: 17487.076 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Organ (production host): kidney / 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: HEAVY CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Organ (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa |
-Protein , 1 types, 1 molecules T
#3: Protein | Mass: 23820.443 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-243 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P13726 |
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-Non-polymers , 4 types, 91 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CAC / | #6: Chemical | ChemComp-03R / | #7: 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: 2.7 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 8000,CACODYLATE, GLYCEROL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.08 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 27, 1999 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→20 Å / Num. all: 24709 / Num. obs: 21938 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.11 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.52→2.63 Å / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DAN USING SEPARATE REPLACEMENTS FOR EA Resolution: 2.52→8 Å / Isotropic thermal model: OVERALL / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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