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Yorodumi- PDB-4x8s: FACTOR VIIA IN COMPLEX WITH THE INHIBITOR 4-BROMO-2-METHOXYPHENOL -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x8s | ||||||
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Title | FACTOR VIIA IN COMPLEX WITH THE INHIBITOR 4-BROMO-2-METHOXYPHENOL | ||||||
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 / response to carbon dioxide / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K ...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 / response to carbon dioxide / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to thyroxine / positive regulation of leukocyte chemotaxis / response to growth hormone / response to cholesterol / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / animal organ regeneration / positive regulation of blood coagulation / 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 / response to estrogen / circadian rhythm / 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: 2.1 Å | ||||||
Authors | Wei, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Discovery of Novel P1 Groups for Coagulation Factor VIIa Inhibition Using Fragment-Based Screening. Authors: Cheney, D.L. / Bozarth, J.M. / Metzler, W.J. / Morin, P.E. / Mueller, L. / Newitt, J.A. / Nirschl, A.H. / Rendina, A.R. / Tamura, J.K. / Wei, A. / Wen, X. / Wurtz, N.R. / Seiffert, D.A. / ...Authors: Cheney, D.L. / Bozarth, J.M. / Metzler, W.J. / Morin, P.E. / Mueller, L. / Newitt, J.A. / Nirschl, A.H. / Rendina, A.R. / Tamura, J.K. / Wei, A. / Wen, X. / Wurtz, N.R. / Seiffert, D.A. / 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 | 4x8s.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x8s.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 4x8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x8s_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 4x8s_full_validation.pdf.gz | 468.4 KB | Display | |
Data in XML | 4x8s_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 4x8s_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/4x8s ftp://data.pdbj.org/pub/pdb/validation_reports/x8/4x8s | 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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Details | chains H & L |
-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) / 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 / Fragment: unp RESIDUES 150-204 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, 282 molecules
#3: Chemical | ChemComp-3Z7 / | ||||
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#4: Chemical | ChemComp-CA / | ||||
#5: Chemical | ChemComp-SO4 / #6: Chemical | #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: 3.83 Å3/Da / Density % sol: 67.92 % |
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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 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 31655 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 31.22 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 6.4 / Rejects: 0 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FACTOR VIIA/LIGAND Resolution: 2.1→26.72 Å / Cor.coef. Fo:Fc: 0.9502 / Cor.coef. Fo:Fc free: 0.9355 / SU R Cruickshank DPI: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.126
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Displacement parameters | Biso max: 105.8 Å2 / Biso mean: 33.31 Å2 / Biso min: 14.99 Å2
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Refine analyze | Luzzati coordinate error obs: 0.219 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→26.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å / Total num. of bins used: 15
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