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- PDB-1zbj: Inferential Structure Determination of the Fyn SH3 domain using N... -

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Entry
Database: PDB / ID: 1zbj
TitleInferential Structure Determination of the Fyn SH3 domain using NOESY data from a 15N,H2 enriched protein
ComponentsProto-oncogene tyrosine-protein kinase FYN
KeywordsTRANSFERASE
Function / homology
Function and homology information


negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / heart process / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Activated NTRK2 signals through FYN / regulation of calcium ion import across plasma membrane ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / heart process / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Activated NTRK2 signals through FYN / regulation of calcium ion import across plasma membrane / Platelet Adhesion to exposed collagen / reelin-mediated signaling pathway / CRMPs in Sema3A signaling / FLT3 signaling through SRC family kinases / G protein-coupled glutamate receptor signaling pathway / activated T cell proliferation / CD4 receptor binding / feeding behavior / positive regulation of protein localization to membrane / Nef and signal transduction / Co-stimulation by CD28 / EPH-Ephrin signaling / natural killer cell activation / DCC mediated attractive signaling / cellular response to L-glutamate / Nephrin family interactions / type 5 metabotropic glutamate receptor binding / CD28 dependent Vav1 pathway / Ephrin signaling / negative regulation of dendritic spine maintenance / dendritic spine maintenance / Regulation of KIT signaling / leukocyte migration / growth factor receptor binding / cellular response to peptide hormone stimulus / phospholipase activator activity / EPHA-mediated growth cone collapse / tau-protein kinase activity / Co-inhibition by CTLA4 / dendrite morphogenesis / Dectin-2 family / negative regulation of T cell activation / peptide hormone receptor binding / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / PECAM1 interactions / CD8 receptor binding / response to amyloid-beta / FCGR activation / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / Role of LAT2/NTAL/LAB on calcium mobilization / cellular response to glycine / CD28 dependent PI3K/Akt signaling / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of protein targeting to membrane / negative regulation of T cell receptor signaling pathway / cellular response to transforming growth factor beta stimulus / detection of mechanical stimulus involved in sensory perception of pain / glial cell projection / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / alpha-tubulin binding / phosphatidylinositol 3-kinase binding / postsynaptic density, intracellular component / ephrin receptor binding / GPVI-mediated activation cascade / phospholipase binding / T cell costimulation / T cell receptor binding / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / peptidyl-tyrosine phosphorylation / EPHB-mediated forward signaling / negative regulation of protein ubiquitination / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / negative regulation of angiogenesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / axon guidance / Cell surface interactions at the vascular wall / protein catabolic process / learning / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / actin filament / response to cocaine / Regulation of signaling by CBL / negative regulation of inflammatory response to antigenic stimulus / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / positive regulation of neuron projection development / negative regulation of protein catabolic process / Degradation of CDH1 / positive regulation of protein localization to nucleus
Similarity search - Function
: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / Src homology 2 domains / SH2 domain ...: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Inferential Structure Determination, Markov Chain Monte Carlo Sampling, Replica-exchange Monte Carlo, Gibbs sampling, Hybrid Monte Carlo, Torsion angle dynamics
AuthorsRieping, 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
DepositionApr 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase FYN


Theoretical massNumber of molelcules
Total (without water)6,7381
Polymers6,7381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10000High posterior probability structures
Representative

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase FYN / P59-FYN / SYN / SLK


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

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Experiment

ExperimentMethod: SOLUTION NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

NMR softwareName: ISD / Version: 1 / Developer: Habeck, Rieping / Classification: refinement
RefinementMethod: Inferential Structure Determination, Markov Chain Monte Carlo Sampling, Replica-exchange Monte Carlo, Gibbs sampling, Hybrid Monte Carlo, Torsion angle dynamics
Software ordinal: 1
NMR ensembleConformer selection criteria: High posterior probability structures
Conformers calculated total number: 10000 / Conformers submitted total number: 20

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