+Open data
-Basic information
Entry | Database: PDB / ID: 1klj | ||||||
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Title | Crystal structure of uninhibited factor VIIa | ||||||
Components | (factor VIIa) x 2 | ||||||
Keywords | HYDROLASE / extrinsic coagulation pathway / serine protease activation / rational drug design / substrate-assisted catalysis | ||||||
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: 2.44 Å | ||||||
Authors | Sichler, K. / Banner, D. / D'Arcy, A. / Hopfner, K.P. / Huber, R. / Bode, W. / Kresse, G.B. / Kopetzki, E. / Brandstetter, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structures of uninhibited factor VIIa link its cofactor and substrate-assisted activation to specific interactions. Authors: Sichler, K. / Banner, D.W. / D'Arcy, A. / Hopfner, K.P. / Huber, R. / Bode, W. / Kresse, G.B. / Kopetzki, E. / Brandstetter, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1klj.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1klj.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 1klj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1klj_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 1klj_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | 1klj_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 1klj_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/1klj ftp://data.pdbj.org/pub/pdb/validation_reports/kl/1klj | HTTPS FTP |
-Related structure data
Related structure data | 1kliSC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 7610.542 Da / Num. of mol.: 1 / Fragment: light chain Source method: isolated from a genetically manipulated source Details: N-terminal truncation / Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08709, coagulation factor VIIa |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-EDO / |
#5: 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: 3.57 Å3/Da / Density % sol: 65.52 % |
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Crystal grow | Temperature: 275 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Ammonium sulphate, glycerol, PEG 400, BICINE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 275K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 2, 2001 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→20 Å / Num. obs: 18853 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.113 |
Reflection shell | Resolution: 2.44→2.5 Å / Rmerge(I) obs: 0.658 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KLI Resolution: 2.44→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.44→20 Å
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Refine LS restraints |
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