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Yorodumi- PDB-2hft: THE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN TISSUE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hft | |||||||||
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Title | THE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN TISSUE FACTOR AT 1.7 ANGSTROMS RESOLUTION | |||||||||
Components | HUMAN TISSUE FACTOR | |||||||||
Keywords | COAGULATION FACTOR | |||||||||
Function / homology | Function and homology information activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / positive regulation of endothelial cell proliferation ...activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / positive regulation of endothelial cell proliferation / positive regulation of interleukin-8 production / phospholipid binding / protein processing / cytokine-mediated signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of angiogenesis / blood coagulation / collagen-containing extracellular matrix / protease binding / positive regulation of cell migration / external side of plasma membrane / positive regulation of gene expression / cell surface / extracellular space / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.69 Å | |||||||||
Authors | Muller, Y.A. / De Vos, A.M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: The crystal structure of the extracellular domain of human tissue factor refined to 1.7 A resolution. Authors: Muller, Y.A. / Ultsch, M.H. / de Vos, A.M. #1: Journal: Biochemistry / Year: 1995 Title: Analysis of the Factor Viia Binding Site on Human Tissue Factor: Effects of Tissue Factor Mutations on the Kinetics and Thermodynamics of Binding Authors: Kelley, R.F. / Costas, K.E. / O'Connell, E.M. / Lazarus, R.A. #2: Journal: Biochemistry / Year: 1994 Title: Structure of the Extracellular Domain of Human Tissue Factor: Location of the Factor Viia Binding Site Authors: Muller, Y.A. / Ultsch, M.H. / Kelley, R.F. / De Vos, A.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hft.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hft.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 2hft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/2hft ftp://data.pdbj.org/pub/pdb/validation_reports/hf/2hft | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 27 |
-Components
#1: Protein | Mass: 24697.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P13726 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Compound details | THE FACTOR VII BINDING SITE WAS IDENTIFIED BY ALA-SCANNING MUTAGENESIS (KELLEY ET AL., 1995; SEE ...THE FACTOR VII BINDING SITE WAS IDENTIFIED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.44 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 49 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 100 K / Method: vapor diffusion, sitting dropDetails: drop contains 0.05 ml of protein solution and 0.01 ml of reservoir solution | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Wavelength: 0.908 Å |
Detector | Type: FUJI FILM / Detector: IMAGE PLATE |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→6 Å / Num. obs: 24199 / % possible obs: 97 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.058 |
Reflection | *PLUS Rmerge(I) obs: 0.058 |
-Processing
Software |
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Refinement | Resolution: 1.69→6 Å / σ(F): 0
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Displacement parameters | Biso mean: 27.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ/X-PLOR / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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