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Yorodumi- PDB-2aer: Crystal Structure of Benzamidine-Factor VIIa/Soluble Tissue Facto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aer | ||||||
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Title | Crystal Structure of Benzamidine-Factor VIIa/Soluble Tissue Factor complex. | ||||||
Components |
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Keywords | BLOOD CLOTTING / Serine Protease / calcium / Magnesium / Zinc / Sodium / Factor VIIa / Tissue Factor / Benzamidine / blood coagulation / clotting / blood / coagulation / clotting factor / coagulation factor | ||||||
Function / homology | Function and homology information activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / 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 ...activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / 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 / NGF-stimulated transcription / response to cholesterol / response to growth hormone / cytokine receptor activity / 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 / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of interleukin-8 production / circadian rhythm / protein processing / phospholipid binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / cytokine-mediated signaling pathway / Golgi lumen / response to estrogen / positive regulation of angiogenesis / blood coagulation / response to estradiol / protease binding / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of gene expression / cell surface / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Isomorphous Replacement / Resolution: 1.87 Å | ||||||
Authors | Bajaj, S.P. / Schmidt, A.E. / Padmanabhan, K. / Bajaj, M.S. / Liesum, A. / Dumas, J. / Prevost, D. / Schreuder, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: High Resolution Structures of p-Aminobenzamidine- and Benzamidine-VIIa/Soluble Tissue Factor: Unpredicted conformation of the 192-193 peptide bond and mapping of Ca2+, Mg2+, Na+ and Zn2+ sites in factor VIIa Authors: Bajaj, S.P. / Schmidt, A.E. / Agah, S. / Bajaj, M.S. / Padmanabhan, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aer.cif.gz | 153.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aer.ent.gz | 116.2 KB | Display | PDB format |
PDBx/mmJSON format | 2aer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aer_validation.pdf.gz | 512.4 KB | Display | wwPDB validaton report |
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Full document | 2aer_full_validation.pdf.gz | 521 KB | Display | |
Data in XML | 2aer_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 2aer_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/2aer ftp://data.pdbj.org/pub/pdb/validation_reports/ae/2aer | HTTPS FTP |
-Related structure data
Related structure data | 2a2qC 2firC 1danS 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
-Coagulation factor ... , 2 types, 2 molecules LH
#1: Protein | Mass: 16359.772 Da / Num. of mol.: 1 / Fragment: Factor VII light chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08709 |
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#2: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: Factor VII heavy chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa |
-Protein , 1 types, 1 molecules T
#3: Protein | Mass: 23374.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P13726 |
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-Sugars , 2 types, 2 molecules
#4: Sugar | ChemComp-GLC / |
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#5: Sugar | ChemComp-FUC / |
-Non-polymers , 7 types, 731 molecules
#6: Chemical | #7: Chemical | ChemComp-CA / #8: Chemical | ChemComp-NA / | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-BEN / | #12: 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: 2.38 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Tris, Sodium Chloride, Calcium Chloride, PEG 4000, ADA, Magnesium Chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→99 Å / Num. all: 59158 / Num. obs: 58300 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.05 |
-Processing
Software |
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Refinement | Method to determine structure: Isomorphous Replacement Starting model: PDB Code: 1DAN Resolution: 1.87→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22.1 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→8 Å
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Refine LS restraints |
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