+Open data
-Basic information
Entry | Database: PDB / ID: 1fyn | ||||||
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Title | PHOSPHOTRANSFERASE | ||||||
Components |
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Keywords | TRANSFERASE / PROTO-ONCOGENE / TYROSINE-PROTEIN KINASE / PHOSPHORYLATION / ATP-BINDING / MYRISTYLATION / SH3 DOMAIN / COMPLEX (PHOSPHOTRANSFERASE-PEPTIDE) | ||||||
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 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / Platelet Adhesion to exposed collagen / CD28 co-stimulation / 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 / Nef and signal transduction / feeding behavior / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / DCC mediated attractive signaling / Nephrin family interactions / dendrite morphogenesis / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / CTLA4 inhibitory signaling / tau-protein kinase activity / phospholipase activator activity / leukocyte migration / EPHA-mediated growth cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / cellular response to platelet-derived growth factor stimulus / cellular response to glycine / Dectin-2 family / glial cell projection / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / phospholipase binding / CD28 dependent PI3K/Akt signaling / response to amyloid-beta / alpha-tubulin binding / Sema3A PAK dependent Axon repulsion / positive regulation of protein targeting to membrane / FCGR activation / 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 / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of protein ubiquitination / negative regulation of inflammatory response to antigenic stimulus / Signaling by ERBB2 / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / EPHB-mediated forward signaling / T cell costimulation / extrinsic component of cytoplasmic side of plasma membrane / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / ephrin receptor binding / 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 / actin filament / axon guidance / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / neuron migration / protein catabolic process / non-specific protein-tyrosine kinase / tau protein binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / non-membrane spanning protein tyrosine kinase activity / negative regulation of protein catabolic process / Signaling by SCF-KIT / positive regulation of neuron projection development / cellular response to hydrogen peroxide / VEGFA-VEGFR2 Pathway / positive regulation of protein localization to nucleus / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / Signaling by CSF1 (M-CSF) in myeloid cells / calcium ion transport / disordered domain specific binding / PIP3 activates AKT signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Musacchio, A. / Saraste, M. / Wilmanns, M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1994 Title: High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides. Authors: Musacchio, A. / Saraste, M. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fyn.cif.gz | 26.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fyn.ent.gz | 16.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fyn ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fyn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6953.491 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: BL21 DE3 / Gene: FYN TYROSINE KINASE / Production host: Escherichia coli (E. coli) / References: UniProt: P06241, EC: 2.7.1.112 |
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#2: Protein/peptide | Mass: 1031.201 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CHEMICALLY SYNTHESIZED |
#3: Water | ChemComp-HOH / |
Compound details | THIS ENTRY CONTAINS COORDINATES OF THE COMPLEX BETWEEN THE SH3 DOMAIN OF FYN TYROSINE KINASE AND A ...THIS ENTRY CONTAINS COORDINATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.2 / Method: vapor diffusion, hanging dropDetails: protein solution is mixed with lyophilized 3BP-2 peptide at a 1:1 molar ratio and subsequently mixed at 1:1(v:v) to reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / % possible obs: 88 % / Rmerge(I) obs: 0.088 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.234 / Rfactor obs: 0.234 / Highest resolution: 2.3 Å Details: THE 3BP2 PEPTIDE LIES ON A CRYSTALLOGRAPHIC TWO-FOLD AXIS, I.E., IT IS DISORDERED. OCCUPANCY OF PEPTIDE ATOMS HAS BEEN SET TO 0.5. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.3 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 2436 / Rfactor obs: 0.171 / Rfactor Rwork: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.011 |