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Yorodumi- PDB-2cez: Phosphorylation of the Cytoplasmic Tail of Tissue Factor and its ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cez | |||||||||
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Title | Phosphorylation of the Cytoplasmic Tail of Tissue Factor and its Role in Modulating Structure and Binding Affinity | |||||||||
Components | TISSUE FACTOR | |||||||||
Keywords | BLOOD CLOTTING / TISSUE FACTOR / PIN1 / WW DOMAIN / BLOOD COAGULATION / GLYCOPROTEIN / LIPOPROTEIN / MEMBRANE / PALMITATE / TRANSMEMBRANE | |||||||||
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 | SOLUTION NMR / simulated annealing | |||||||||
Authors | Sen, M. / Agrawal, S. / Craft, J.W. / Ruf, W. / Legge, G.B. | |||||||||
Citation | Journal: Open Spectrosc J / Year: 2009 Title: Spectroscopic Characterization of Successive Phosphorylation of the Tissue Factor Cytoplasmic Region. Authors: Sen, M. / Herzik, M. / Craft, J.W. / Creath, A.L. / Agrawal, S. / Ruf, W. / Legge, G.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cez.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cez.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 2cez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/2cez ftp://data.pdbj.org/pub/pdb/validation_reports/ce/2cez | HTTPS FTP |
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-Related structure data
Related structure data | 2cefC 2cehC 2cfjC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2143.297 Da / Num. of mol.: 1 Fragment: TISSUE FACTOR CYTOPLASMIC DOMAIN, RESIDUES 277-295 Source method: obtained synthetically Details: THIS PEPTIDE IS PHOSPHORYLATED AT THE POSITION OF SER253 Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P13726 | ||
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Compound details | INITIATES BLOOD COAGULATIOSequence details | CYTOPLASMI | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE SINGLE 253 PHOSPHORYLATED TFCD PEPTIDE NMR STRUCTURES WERE CALCULATED USING 2D HOMONUCLEAR NMR SPECTROSCOPY METHODS. |
-Sample preparation
Details | Contents: 90% WATER 10% D2O |
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Sample conditions | Ionic strength: 0 / pH: 6.0 / Pressure: 1.0 atm / Temperature: 285.0 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: INITIAL NMR STRUCTURES WERE CALCULATED BY DYANA, WHICH INCLUDES MODIFIED SEP RESIDUE, PHOSPHORYLATED SER, CRAFT AND LEGGE, 2005, J.BIOL MOL.NMR. TOP10 ANNEALLED STRUCTURES THEN FURTHER MINIMIZED VIA AMBER 8.0. | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST POTENTIAL ENERGY ENSEMBLES Conformers calculated total number: 50 / Conformers submitted total number: 10 |