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Yorodumi- PDB-5tqe: Factor VIIa in complex with the inhibitor (5R)-5-[(1-aminoisoquin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tqe | ||||||
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Title | Factor VIIa in complex with the inhibitor (5R)-5-[(1-aminoisoquinolin-6-yl)amino]-19-(cyclopropylsulfonyl)-3-methyl-13-oxa-3,15-diazatricyclo[14.3.1.1~6,10~]henicosa-1(20),6(21),7,9,16,18-hexaene-4,14-dione | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wei, A. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: Design and Synthesis of Novel Meta-Linked Phenylglycine Macrocyclic FVIIa Inhibitors. Authors: Richter, J.M. / Cheney, D.L. / Bates, J.A. / Wei, A. / Luettgen, J.M. / Rendina, A.R. / Harper, T.M. / Narayanan, R. / Wong, P.C. / Seiffert, D. / 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 | 5tqe.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tqe.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 5tqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tqe_validation.pdf.gz | 831.4 KB | Display | wwPDB validaton report |
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Full document | 5tqe_full_validation.pdf.gz | 833.7 KB | Display | |
Data in XML | 5tqe_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 5tqe_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/5tqe ftp://data.pdbj.org/pub/pdb/validation_reports/tq/5tqe | HTTPS FTP |
-Related structure data
Related structure data | 5tqfC 5tqgC 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 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, 377 molecules
#3: Chemical | ChemComp-7KQ / ( | ||||
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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: 3.91 Å3/Da / Density % sol: 68.52 % |
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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: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 43075 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.072 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 4.3 / Num. unique all: 4115 / Rejects: 0 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAN Resolution: 1.9→34.46 Å / Cor.coef. Fo:Fc: 0.9503 / Cor.coef. Fo:Fc free: 0.9359 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.103
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Displacement parameters | Biso max: 102.57 Å2 / Biso mean: 27.72 Å2 / Biso min: 9.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.215 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→34.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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