+Open data
-Basic information
Entry | Database: PDB / ID: 2d8j | ||||||
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Title | Solution structure of the SH3 domain of Fyn-related kinase | ||||||
Components | fyn-related kinase | ||||||
Keywords | TRANSFERASE / SH3 domain / Fyn-related kinase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Regulation of PTEN stability and activity / extrinsic component of cytoplasmic side of plasma membrane / Neutrophil degranulation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase activity / cell differentiation / phosphorylation / signaling receptor binding ...Regulation of PTEN stability and activity / extrinsic component of cytoplasmic side of plasma membrane / Neutrophil degranulation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase activity / cell differentiation / phosphorylation / signaling receptor binding / innate immune response / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X.R. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Solution structure of the SH3 domain of Fyn-related kinase Authors: Qin, X.R. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d8j.cif.gz | 437 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d8j.ent.gz | 381.6 KB | Display | PDB format |
PDBx/mmJSON format | 2d8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/2d8j ftp://data.pdbj.org/pub/pdb/validation_reports/d8/2d8j | 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: 8333.002 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: cell free protein synthesis / Gene: FrK / Plasmid: P050425-22 References: GenBank: 31542823, UniProt: Q922K9*PLUS, EC: 2.7.1.112 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.17mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: JEOL ECA / Manufacturer: JEOL / Model: ECA / Field strength: 800 MHz |
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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 |