+Open data
-Basic information
Entry | Database: PDB / ID: 1kli | ||||||
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Title | Cofactor-and substrate-assisted activation of factor VIIa | ||||||
Components | (factor VIIaCoagulation factor VII) 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 / positive regulation of leukocyte chemotaxis / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / 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 / signaling receptor binding / serine-type endopeptidase activity / 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: 1.69 Å | ||||||
Authors | Sichler, K. / Banner, D.W. / 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 Structure 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 | 1kli.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kli.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/1kli ftp://data.pdbj.org/pub/pdb/validation_reports/kl/1kli | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules LH
#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 |
-Non-polymers , 5 types, 306 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-BEN / | #6: Chemical | ChemComp-GOL / | #7: 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 | 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 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 170 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→20 Å / Num. obs: 59659 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.057 |
Reflection shell | Resolution: 1.69→1.75 Å / % possible all: 87.6 |
Reflection | *PLUS % possible obs: 98.3 % / Redundancy: 9.33 % / Num. measured all: 556747 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 87.6 % / Rmerge(I) obs: 0.652 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.69→20 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.2245 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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