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Yorodumi- PDB-2cef: Phosphorylation of the Cytoplasmic Tail of Tissue Factor and its ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cef | |||||||||
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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 / COAGULATION PROTEIN / PIN1 / WW DOMAIN / BLOOD COAGULATION PROTEIN / LIPOPROTEIN / PALMITATE / TRANSMEMBRANE | |||||||||
Function / homology | Function and homology information activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / 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 blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / 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 / protein processing / phospholipid binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / cytokine-mediated signaling pathway / positive regulation of angiogenesis / blood coagulation / protease binding / collagen-containing extracellular matrix / 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 / DYANA AMBER 8.0 | |||||||||
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 | 2cef.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cef.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 2cef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/2cef ftp://data.pdbj.org/pub/pdb/validation_reports/ce/2cef | HTTPS FTP |
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-Related structure data
Related structure data | 2cehC 2cezC 2cfjC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
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: 2223.276 Da / Num. of mol.: 1 Fragment: TISSUE FACTOR CYTOPLASMIC DOMAIN, RESIDUES 277-295 Source method: obtained synthetically / Details: SER253 AND SER258 ARE PHOSPHORYLATED / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P13726 |
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Sequence details | THIS IS ONLY THE CYTOPLASMI |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE NMR STRUCTURE OF THE PHOSPHORYLATED PEPTIDE WAS DETERMINED USING HOMONUCLEAR 2D NMR SPECTROSCOPY METHODS. |
-Sample preparation
Details | Contents: 90% WATER 10% D2O |
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Sample conditions | Ionic strength: 0 / pH: 6 / Temperature: 285.0 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DYANA AMBER 8.0 / 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 ...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 |