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Yorodumi- PDB-5pav: Crystal Structure of Factor VIIa in complex with N-(6-aminopyridi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5pav | ||||||
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Title | Crystal Structure of Factor VIIa in complex with N-(6-aminopyridin-3-yl)-5-hydroxy-1-phenylpyrazole-4-carboxamide | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Stihle, M. / Mayweg, A. / Roever, S. / Rudolph, M.G. | ||||||
Citation | Journal: To be published Title: Crystal Structure of a Factor VIIa complex Authors: Mayweg, A. / Roever, S. / Rudolph, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5pav.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5pav.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 5pav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5pav_validation.pdf.gz | 712.6 KB | Display | wwPDB validaton report |
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Full document | 5pav_full_validation.pdf.gz | 720.6 KB | Display | |
Data in XML | 5pav_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 5pav_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/5pav ftp://data.pdbj.org/pub/pdb/validation_reports/pa/5pav | HTTPS FTP |
-Group deposition
ID | G_1002015 (25 entries) |
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Title | Crystal Structures of Factor VIIa Complexes |
Type | undefined |
Description | Crystal Structures of Factor VIIa Complexes |
-Related structure data
Similar structure data |
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-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 AC
#1: Protein | Mass: 6984.911 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08709, coagulation factor VIIa |
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#2: 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: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08709, coagulation factor VIIa |
-Non-polymers , 6 types, 458 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CA / | #6: Chemical | #7: Chemical | ChemComp-7ZM / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Mosaicity: 0.783 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 19, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.24→50 Å / Num. obs: 114725 / % possible obs: 75.9 % / Redundancy: 8 % / Biso Wilson estimate: 18.654 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1.001 / Net I/av σ(I): 27.279 / Net I/σ(I): 13.2 / Num. measured all: 923374 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse model Resolution: 1.4→33.65 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: the numbering follows that of the unprocessed precursor. the ligand may have occupancy less than 1. Trp424 flips underneath the 5-Hydroxy-1H-pyrazole. The main-chain around Trp424 has at ...Details: the numbering follows that of the unprocessed precursor. the ligand may have occupancy less than 1. Trp424 flips underneath the 5-Hydroxy-1H-pyrazole. The main-chain around Trp424 has at least two conformations and is largely disordered. several water molecules have been modeled with occupancies less than 1 and adopt mutually exclusive positions.
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 136.76 Å2 / Biso mean: 26.37 Å2 / Biso min: 8.59 Å2
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Refinement step | Cycle: final / Resolution: 1.4→33.65 Å
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LS refinement shell | Resolution: 1.4→1.48 Å / Total num. of bins used: 9
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