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- PDB-1fyn: PHOSPHOTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1fyn
TitlePHOSPHOTRANSFERASE
Components
  • 3BP-2
  • PHOSPHOTRANSFERASE FYN
KeywordsTRANSFERASE / PROTO-ONCOGENE / TYROSINE-PROTEIN KINASE / PHOSPHORYLATION / ATP-BINDING / MYRISTYLATION / SH3 DOMAIN / COMPLEX (PHOSPHOTRANSFERASE-PEPTIDE)
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 / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / 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 / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / reelin-mediated signaling pathway / Platelet Adhesion to exposed collagen / CRMPs in Sema3A signaling / G protein-coupled glutamate receptor signaling pathway / FLT3 signaling through SRC family kinases / activated T cell proliferation / positive regulation of protein localization to membrane / type 5 metabotropic glutamate receptor binding / CD4 receptor binding / Nef and signal transduction / cellular response to L-glutamate / feeding behavior / Co-stimulation by CD28 / Nephrin family interactions / DCC mediated attractive signaling / EPH-Ephrin signaling / natural killer cell activation / negative regulation of dendritic spine maintenance / Ephrin signaling / CD28 dependent Vav1 pathway / dendritic spine maintenance / growth factor receptor binding / cellular response to peptide hormone stimulus / tau-protein kinase activity / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / dendrite morphogenesis / peptide hormone receptor binding / CD8 receptor binding / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / PECAM1 interactions / response to amyloid-beta / cellular response to glycine / FCGR activation / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / glial cell projection / CD28 dependent PI3K/Akt signaling / positive regulation of protein targeting to membrane / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ephrin receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / alpha-tubulin binding / cellular response to transforming growth factor beta stimulus / postsynaptic density, intracellular component / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / T cell receptor binding / phosphatidylinositol 3-kinase binding / phospholipase binding / GPVI-mediated activation cascade / ephrin receptor binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / negative regulation of protein ubiquitination / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / peptidyl-tyrosine phosphorylation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / Cell surface interactions at the vascular wall / learning / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / actin filament / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / protein catabolic process / Signaling by SCF-KIT / G protein-coupled receptor binding / positive regulation of neuron projection development / negative regulation of protein catabolic process / modulation of chemical synaptic transmission / positive regulation of protein localization to nucleus / VEGFA-VEGFR2 Pathway / tau protein binding
Similarity search - Function
: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. ...: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMusacchio, A. / Saraste, M. / Wilmanns, M.
CitationJournal: 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
DepositionMay 17, 1995Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOTRANSFERASE FYN
B: 3BP-2


Theoretical massNumber of molelcules
Total (without water)7,9852
Polymers7,9852
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.000, 43.300, 65.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PHOSPHOTRANSFERASE FYN / PROTO-ONCOGENE TYROSINE KINASE


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
#2: Protein/peptide 3BP-2


Mass: 1031.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CHEMICALLY SYNTHESIZED
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENTRY CONTAINS COORDINATES OF THE COMPLEX BETWEEN THE SH3 DOMAIN OF FYN TYROSINE KINASE AND A ...THIS ENTRY CONTAINS COORDINATES OF THE COMPLEX BETWEEN THE SH3 DOMAIN OF FYN TYROSINE KINASE AND A 10-RESIDUE SYNTHETIC PEPTIDE WITH THE SEQUENCE, PPAYPPPPPVP.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.86 %
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop
Details: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMprotein1drop
210 mMTris-HCl1drop
3270 mM1dropNaCl
490 mMsodium citrate1reservoir
590 mMBis-Tris propane1reservoir
60.9 mMdithiothreitol1reservoir
70.9 mMEDTA1reservoir
80.9 mM1reservoirNaN3
938-42 %satammonium sulfate1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 88 % / Rmerge(I) obs: 0.088

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor 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 stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55 0 0 37 92
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.033
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
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

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