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Yorodumi- PDB-2a2q: Complex of Active-site Inhibited Human Coagulation Factor VIIa wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a2q | ||||||
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Title | Complex of Active-site Inhibited Human Coagulation Factor VIIa with Human Soluble Tissue Factor in the Presence of Ca2+, Mg2+, Na+, and Zn2+ | ||||||
Components |
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Keywords | HYDROLASE/BLOOD CLOTTING / Factor VIIa / Soluble Tissue Factor / Mg2+ / Ca2+ / Na+ / Zn2+ / HYDROLASE-BLOOD CLOTTING COMPLEX | ||||||
Function / homology | Function and homology information activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / 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 plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / 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 / 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 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 / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of interleukin-8 production / phospholipid binding / protein processing / Golgi lumen / cytokine-mediated signaling pathway / circadian rhythm / response to estrogen / positive regulation of angiogenesis / activation of cysteine-type endopeptidase activity involved in apoptotic process / blood coagulation / response to estradiol / collagen-containing extracellular matrix / protease binding / vesicle / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bajaj, S.P. / Bajaj, M. / Schmidt, A.E. / Padmanabhan, K. | ||||||
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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Remark 999 | SEQUENCE The heavy chain H has been numbered in accordance with chymotrypsin numbering | ||||||
Remark 600 | HETEROGEN p-aminobenzamidine is a reversible S1 site inhibitor of serine proteases |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a2q.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a2q.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 2a2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/2a2q ftp://data.pdbj.org/pub/pdb/validation_reports/a2/2a2q | HTTPS FTP |
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-Related structure data
Related structure data | 2aerC 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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Details | Factor VIIa, a serine protease in blood coagulation, binds to its cofactor, tissue factor in a 1:1 complex |
-Components
-Coagulation factor ... , 2 types, 2 molecules LH
#1: Protein | Mass: 17487.076 Da / Num. of mol.: 1 / Fragment: Light chain, residues 61-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: PLASMID / Gene: F7 / Plasmid: pMon3360b / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P08709 |
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#2: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: Heavy chain, residues 213-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: PLASMID / Gene: F7 / Plasmid: pMon3360b / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P08709, coagulation factor VIIa |
-Protein , 1 types, 1 molecules T
#3: Protein | Mass: 23302.949 Da / Num. of mol.: 1 / Fragment: residues 38-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: PLASMID / Gene: F3 / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / 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, 738 molecules
#6: Chemical | #7: Chemical | ChemComp-CA / #8: Chemical | ChemComp-NA / | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-PBZ / | #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: 2.41 Å3/Da / Density % sol: 45.42 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: PEG 4000, magnesium chloride, sodium chloride, calcium chloride, zinc chloride, Tris-HCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Apr 11, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→90 Å / Num. obs: 60071 / % possible obs: 90 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.209 / % possible all: 65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DAN Resolution: 1.8→90 Å / Data cutoff high absF: 1.8 / Data cutoff low absF: 8 / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→90 Å
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Refine LS restraints |
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