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Yorodumi- PDB-4ng9: Factor viia in complex with the inhibitor (2R)-2-[(1-aminoisoquin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ng9 | ||||||
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Title | Factor viia in complex with the inhibitor (2R)-2-[(1-aminoisoquinolin-6-yl)amino]-2-[3-ethoxy-4-(propan-2-yloxy)phenyl]-n-(3-sulfamoylbenzyl)ethanamide | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / GLYCOPROTEIN / HYDROLASE / SERINE PROTEASE / PLASMA / BLOOD COAGULATION FACTOR / PROTEIN INHIBITOR COMPLEX / CALCIUM-BINDING / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wei, A. / Anumula, R. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2014 Title: Design and Synthesis of Phenylpyrrolidine Phenylglycinamides As Highly Potent and Selective TF-FVIIa Inhibitors. Authors: Zhang, X. / Jiang, W. / Jacutin-Porte, S. / Glunz, P.W. / Zou, Y. / Cheng, X. / Nirschl, A.H. / Wurtz, N.R. / Luettgen, J.M. / Rendina, A.R. / Luo, G. / Harper, T.M. / Wei, A. / Anumula, R. ...Authors: Zhang, X. / Jiang, W. / Jacutin-Porte, S. / Glunz, P.W. / Zou, Y. / Cheng, X. / Nirschl, A.H. / Wurtz, N.R. / Luettgen, J.M. / Rendina, A.R. / Luo, G. / Harper, T.M. / Wei, A. / Anumula, R. / Cheney, D.L. / Knabb, R.M. / Wong, P.C. / Wexler, R.R. / Priestley, E.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ng9.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ng9.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ng9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ng9_validation.pdf.gz | 822.8 KB | Display | wwPDB validaton report |
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Full document | 4ng9_full_validation.pdf.gz | 824 KB | Display | |
Data in XML | 4ng9_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 4ng9_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/4ng9 ftp://data.pdbj.org/pub/pdb/validation_reports/ng/4ng9 | HTTPS FTP |
-Related structure data
Related structure data | 4ngaC 1danS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules HL
#1: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 6030.827 Da / Num. of mol.: 1 / Fragment: UKNP residues 150-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709 |
-Non-polymers , 5 types, 265 molecules
#3: Chemical | ChemComp-2KE / ( | ||||
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#4: Chemical | ChemComp-CA / | ||||
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / | #7: 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: 3.9 Å3/Da / Density % sol: 68.44 % |
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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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: May 21, 2004 / Details: MICROMAX CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 28178 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 31.58 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 5.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DAN Resolution: 2.2→19.89 Å / Cor.coef. Fo:Fc: 0.9392 / Cor.coef. Fo:Fc free: 0.9169 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.21 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.17
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Displacement parameters | Biso max: 114.85 Å2 / Biso mean: 30.8593 Å2 / Biso min: 10.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.245 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 12
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