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Yorodumi- PDB-1zbj: Inferential Structure Determination of the Fyn SH3 domain using N... -
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-Basic information
Entry | Database: PDB / ID: 1zbj | ||||||
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Title | Inferential Structure Determination of the Fyn SH3 domain using NOESY data from a 15N,H2 enriched protein | ||||||
Components | Proto-oncogene tyrosine-protein kinase FYN | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / growth factor receptor binding / regulation of glutamate receptor signaling pathway ...response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / growth factor receptor binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Platelet Adhesion to exposed collagen / CD28 co-stimulation / G protein-coupled glutamate receptor signaling pathway / positive regulation of protein localization to membrane / activated T cell proliferation / CRMPs in Sema3A signaling / positive regulation of cysteine-type endopeptidase activity / FLT3 signaling through SRC family kinases / negative regulation of dendritic spine maintenance / feeding behavior / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / Nephrin family interactions / DCC mediated attractive signaling / EPH-Ephrin signaling / dendrite morphogenesis / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / tau-protein kinase activity / CTLA4 inhibitory signaling / phospholipase activator activity / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / glial cell projection / Sema3A PAK dependent Axon repulsion / FCGR activation / cellular response to glycine / alpha-tubulin binding / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / forebrain development / Signaling by ERBB2 / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / FCGR3A-mediated IL10 synthesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / learning / axon guidance / actin filament / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / modulation of chemical synaptic transmission / tau protein binding / protein catabolic process / Signaling by SCF-KIT / Schaffer collateral - CA1 synapse / negative regulation of protein catabolic process / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / cellular response to hydrogen peroxide / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Aberrant PI3K in Cancer / disordered domain specific binding / calcium ion transport / DAP12 signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / Inferential Structure Determination, Markov Chain Monte Carlo Sampling, Replica-exchange Monte Carlo, Gibbs sampling, Hybrid Monte Carlo, Torsion angle dynamics | ||||||
Authors | Rieping, W. / Habeck, M. / Nilges, M. | ||||||
Citation | Journal: Science / Year: 2005 Title: Inferential Structure Determination Authors: Rieping, W. / Habeck, M. / Nilges, M. #1: Journal: J.Biomol.NMR / Year: 1998 Title: Some NMR Experiments and a Structure Determination Employing a [15N,2H] Enriched Protein Authors: Mal, T.K. / Matthews, S.J. / Kovacs, H. / Campbell, I.D. / Boyd, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zbj.cif.gz | 358.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zbj.ent.gz | 298.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/1zbj ftp://data.pdbj.org/pub/pdb/validation_reports/zb/1zbj | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6738.284 Da / Num. of mol.: 1 / Fragment: SH3 domain, Residues 83-141 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Production host: Escherichia coli (E. coli) / References: UniProt: P06241, EC: 2.7.1.112 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
-Processing
NMR software | Name: ISD / Version: 1 / Developer: Habeck, Rieping / Classification: refinement |
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Refinement | Method: Inferential Structure Determination, Markov Chain Monte Carlo Sampling, Replica-exchange Monte Carlo, Gibbs sampling, Hybrid Monte Carlo, Torsion angle dynamics Software ordinal: 1 |
NMR ensemble | Conformer selection criteria: High posterior probability structures Conformers calculated total number: 10000 / Conformers submitted total number: 20 |