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Yorodumi- PDB-1qfk: STRUCTURE OF HUMAN FACTOR VIIA AND ITS IMPLICATIONS FOR THE TRIGG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qfk | |||||||||
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Title | STRUCTURE OF HUMAN FACTOR VIIA AND ITS IMPLICATIONS FOR THE TRIGGERING OF BLOOD COAGULATION | |||||||||
Components | (COAGULATION FACTOR VIIA ...) x 2 | |||||||||
Keywords | hydrolase/hydrolase inhibitor / BLOOD COAGULATION / SERINE PROTEASE / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Pike, A.C.W. / Brzozowski, A.M. / Roberts, S.M. / Olsen, O.H. / Persson, E. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Structure of human factor VIIa and its implications for the triggering of blood coagulation. Authors: Pike, A.C. / Brzozowski, A.M. / Roberts, S.M. / Olsen, O.H. / Persson, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qfk.cif.gz | 93.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qfk.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qfk_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1qfk_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1qfk_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 1qfk_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/1qfk ftp://data.pdbj.org/pub/pdb/validation_reports/qf/1qfk | HTTPS FTP |
-Related structure data
Related structure data | 1danS S: Starting model for refinement |
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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 VIIA ... , 2 types, 2 molecules LH
#1: Protein | Mass: 11383.764 Da / Num. of mol.: 1 / Fragment: UNP residues 109-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Plasmid: ZEM219B / Cell line (production host): BHK570 / Cellular location (production host): SECRETED / Culture collection (production host): ATCC CRL 1632 / Gene (production host): FACTOR VII / Organelle (production host): NUCLEUS / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Plasmid: ZEM219B / Cell line (production host): BHK570 / Cellular location (production host): SECRETED / Culture collection (production host): ATCC CRL 1632 / Gene (production host): FACTOR VII / Organelle (production host): NUCLEUS / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P08709, coagulation factor VIIa |
-Sugars , 3 types, 3 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-GLC / |
#5: Sugar | ChemComp-FUC / |
-Non-polymers , 3 types, 86 molecules
#6: Chemical | ChemComp-0Z6 / |
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#7: Chemical | ChemComp-CA / |
#8: Water | ChemComp-HOH / |
-Details
Nonpolymer details | THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PHE-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PHE-ARG-CHLOROMETH |
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Sequence details | NO SIGNAL SEQUENCE RESIDUES 1-44 OF MATURE PROTEIN ARE NOT PRESENT IN EXPRESSION CONSTRUCT, ...NO SIGNAL SEQUENCE RESIDUES 1-44 OF MATURE PROTEIN ARE NOT PRESENT IN EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 50MM NACL, 10MM CACL2, 3.5-3.7M SODIUM FORMATE IN 100MM TRIS PH 8.5, pH 8.50 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8342 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8342 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→35 Å / Num. obs: 16157 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 70 Å2 / Rsym value: 0.056 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 3 / % possible all: 79.4 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 35 Å / % possible obs: 95.4 % / Redundancy: 4 % / Num. measured all: 238127 / Rmerge(I) obs: 0.056 / Biso Wilson estimate: 70 Å2 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.85 Å / % possible obs: 79.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DAN Resolution: 2.8→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.57 / ESU R Free: 0.34 Details: XPLOR BULK SOLVENT CORRECTION USED INSTEAD OF REFMAC DEFAULT CORRECTION THE MAINCHAIN OF RESIDUES L104-L111 EXHIBITS STATIC DISORDER AND HAS BEEN MODELED IN TWO ALTERNATE CONFORMATIONS
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Displacement parameters | Biso mean: 56.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→35 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 35 Å / Rfactor obs: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |