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Yorodumi- PDB-2dm0: Solution structure of the SH2 domain of human Tyrosine-protein ki... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dm0 | ||||||
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Title | Solution structure of the SH2 domain of human Tyrosine-protein kinase TXK | ||||||
Components | Tyrosine-protein kinase TXKTXK (gene) | ||||||
Keywords | TRANSFERASE / TEC family kinase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information positive regulation of type II interferon-mediated signaling pathway / regulation of platelet activation / tissue regeneration / activation of phospholipase C activity / peptidyl-tyrosine autophosphorylation / transmembrane receptor protein tyrosine kinase activity / FCERI mediated Ca+2 mobilization / integrin-mediated signaling pathway / positive regulation of cytokine production / non-specific protein-tyrosine kinase ...positive regulation of type II interferon-mediated signaling pathway / regulation of platelet activation / tissue regeneration / activation of phospholipase C activity / peptidyl-tyrosine autophosphorylation / transmembrane receptor protein tyrosine kinase activity / FCERI mediated Ca+2 mobilization / integrin-mediated signaling pathway / positive regulation of cytokine production / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of type II interferon production / T cell receptor signaling pathway / regulation of gene expression / protein tyrosine kinase activity / adaptive immune response / protein autophosphorylation / protein phosphorylation / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Endo, H. / Hayashi, F. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the SH2 domain of human Tyrosine-protein kinase TXK Authors: Endo, H. / Hayashi, F. / Yoshida, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dm0.cif.gz | 762.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dm0.ent.gz | 661.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dm0 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dm0 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14202.865 Da / Num. of mol.: 1 / Fragment: sh2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: TXK / Plasmid: P050704-08 / Production host: Cell free synthesis References: UniProt: P42681, non-specific protein-tyrosine kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: spectrometer_id 1 for 3D_15N-separated_NOESY; spectrometer_id 2 for 3D_13C-separated_NOESY |
-Sample preparation
Details | Contents: 1.06mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |