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Yorodumi- PDB-4na9: Factor VIIa in complex with the inhibitor 3'-amino-5'-[(2s,4r)-6-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4na9 | ||||||
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Title | Factor VIIa in complex with the inhibitor 3'-amino-5'-[(2s,4r)-6-carbamimidoyl-4-phenyl-1,2,3,4-tetrahydroquinolin-2-yl]biphenyl-2-carboxylic acid | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / serine protease / hydrolase / plasma / blood coagulation factor / protein inhibitor complex / calcium-binding / glycoprotein / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 ...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 / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / 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 / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / protein processing / Golgi lumen / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Wei, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Tetrahydroquinoline Derivatives as Potent and Selective Factor XIa Inhibitors. Authors: Quan, M.L. / Wong, P.C. / Wang, C. / Woerner, F. / Smallheer, J.M. / Barbera, F.A. / Bozarth, J.M. / Brown, R.L. / Harpel, M.R. / Luettgen, J.M. / Morin, P.E. / Peterson, T. / Ramamurthy, V. ...Authors: Quan, M.L. / Wong, P.C. / Wang, C. / Woerner, F. / Smallheer, J.M. / Barbera, F.A. / Bozarth, J.M. / Brown, R.L. / Harpel, M.R. / Luettgen, J.M. / Morin, P.E. / Peterson, T. / Ramamurthy, V. / Rendina, A.R. / Rossi, K.A. / Watson, C.A. / Wei, A. / Zhang, G. / Seiffert, D. / Wexler, R.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4na9.cif.gz | 80.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4na9.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 4na9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4na9_validation.pdf.gz | 785.3 KB | Display | wwPDB validaton report |
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Full document | 4na9_full_validation.pdf.gz | 789.1 KB | Display | |
Data in XML | 4na9_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 4na9_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/4na9 ftp://data.pdbj.org/pub/pdb/validation_reports/na/4na9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: 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 / Production host: Cricetinae (hamsters) / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 6030.827 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Cricetinae (hamsters) / References: UniProt: P08709, coagulation factor VIIa |
#3: Chemical | ChemComp-1T7 / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES, pH 6.0, 20 mM CACL2, 17.5%(W/V) PEG 6000, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 12, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. obs: 23744 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 33.89 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.24→2.46 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 7.5 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FACTOR VIIA/LIGAND Resolution: 2.24→19.53 Å / Cor.coef. Fo:Fc: 0.9098 / Cor.coef. Fo:Fc free: 0.8949 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.256 / SU Rfree Blow DPI: 0.2 / SU Rfree Cruickshank DPI: 0.195
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Displacement parameters | Biso mean: 35.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→19.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.35 Å / Total num. of bins used: 11
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