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Yorodumi- PDB-5i46: Factor VIIA in complex with the inhibitor (2R,15R)-2-[(1-aminoiso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i46 | ||||||
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Title | Factor VIIA in complex with the inhibitor (2R,15R)-2-[(1-aminoisoquinolin-6-yl)amino]-8-fluoro-7-hydroxy-4,15,17-trimethyl-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaene-3,12-dione | ||||||
Components | (Coagulation factor VII ...) x 2 | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Wei, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Atropisomer Control in Macrocyclic Factor VIIa Inhibitors. Authors: Glunz, P.W. / Mueller, L. / Cheney, D.L. / Ladziata, V. / Zou, Y. / Wurtz, N.R. / Wei, A. / 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 | 5i46.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i46.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 5i46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i46_validation.pdf.gz | 787.4 KB | Display | wwPDB validaton report |
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Full document | 5i46_full_validation.pdf.gz | 790.4 KB | Display | |
Data in XML | 5i46_validation.xml.gz | 16 KB | Display | |
Data in CIF | 5i46_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/5i46 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/5i46 | 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 on special symmetry positions |
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-Components
-Coagulation factor VII ... , 2 types, 2 molecules HL
#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 |
-Non-polymers , 5 types, 215 molecules
#3: Chemical | ChemComp-67O / ( | ||||
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#4: Chemical | ChemComp-CA / | ||||
#5: Chemical | #6: Chemical | ChemComp-MES / | #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: 68.47 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 33633 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 34.03 Å2 / Rsym value: 0.096 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.8 / Rejects: 0 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAN Resolution: 2.06→36.98 Å / Cor.coef. Fo:Fc: 0.9188 / Cor.coef. Fo:Fc free: 0.9087 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.164 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.14
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Displacement parameters | Biso max: 117.65 Å2 / Biso mean: 36.71 Å2 / Biso min: 17.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.296 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.06→36.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.12 Å / Total num. of bins used: 17
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