[English] 日本語
Yorodumi- PDB-5u6j: Factor VIIa in complex with the inhibitor 3-{[(2R)-17-ethyl-4-met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u6j | ||||||
---|---|---|---|---|---|---|---|
Title | Factor VIIa in complex with the inhibitor 3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan-2-yl)sulfonyl]-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaen-2-yl]amino}benzamide | ||||||
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: 2.3 Å | ||||||
Authors | Wei, A. | ||||||
Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2017 Title: Neutral macrocyclic factor VIIa inhibitors. Authors: Wurtz, N.R. / Parkhurst, B.L. / DeLucca, I. / Glunz, P.W. / Jiang, W. / Zhang, X. / Cheney, D.L. / Bozarth, J.M. / Rendina, A.R. / Wei, A. / Harper, T. / Luettgen, J.M. / Wu, Y. / Wong, P.C. ...Authors: Wurtz, N.R. / Parkhurst, B.L. / DeLucca, I. / Glunz, P.W. / Jiang, W. / Zhang, X. / Cheney, D.L. / Bozarth, J.M. / Rendina, A.R. / Wei, A. / Harper, T. / Luettgen, J.M. / Wu, Y. / Wong, P.C. / Seiffert, D.A. / Wexler, R.R. / Priestley, E.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5u6j.cif.gz | 85.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5u6j.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 5u6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u6j_validation.pdf.gz | 811.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5u6j_full_validation.pdf.gz | 813.6 KB | Display | |
Data in XML | 5u6j_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 5u6j_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/5u6j ftp://data.pdbj.org/pub/pdb/validation_reports/u6/5u6j | HTTPS FTP |
-Related structure data
Related structure data | 1danS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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 |
---|---|
#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, 227 molecules
#3: Chemical | ChemComp-82J / | ||||
---|---|---|---|---|---|
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.66 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 24829 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 38.08 Å2 / Rsym value: 0.107 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 14 % / Mean I/σ(I) obs: 4.8 / Rsym value: 0.486 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAN Resolution: 2.3→25.53 Å / Cor.coef. Fo:Fc: 0.9338 / Cor.coef. Fo:Fc free: 0.9161 / SU R Cruickshank DPI: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.222 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.176
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.48 Å2 / Biso mean: 32.32 Å2 / Biso min: 10.74 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.253 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→25.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 12
|