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- PDB-3a4o: Lyn kinase domain -

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Basic information

Entry
Database: PDB / ID: 3a4o
TitleLyn kinase domain
ComponentsTyrosine-protein kinase Lyn
KeywordsTRANSFERASE / Src family / kinase domain / Alternative splicing / ATP-binding / Host-virus interaction / Kinase / Lipoprotein / Myristate / Nucleotide-binding / Palmitate / Phosphoprotein / Polymorphism / Proto-oncogene / Tyrosine-protein kinase
Function / homology
Function and homology information


C-X-C chemokine receptor CXCR4 signaling pathway / response to sterol depletion / positive regulation of mast cell proliferation / regulation of monocyte chemotaxis / regulation of mast cell activation / eosinophil differentiation / negative regulation of mast cell proliferation / tolerance induction to self antigen / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway ...C-X-C chemokine receptor CXCR4 signaling pathway / response to sterol depletion / positive regulation of mast cell proliferation / regulation of monocyte chemotaxis / regulation of mast cell activation / eosinophil differentiation / negative regulation of mast cell proliferation / tolerance induction to self antigen / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / Fc receptor mediated inhibitory signaling pathway / negative regulation of intracellular signal transduction / regulation of B cell receptor signaling pathway / negative regulation of B cell receptor signaling pathway / negative regulation of toll-like receptor 2 signaling pathway / positive regulation of oligodendrocyte progenitor proliferation / integrin alpha2-beta1 complex / glycosphingolipid binding / immune response-regulating cell surface receptor signaling pathway / Assembly and Release of Dengue Virus Virions / regulation of mast cell degranulation / platelet degranulation / negative regulation of toll-like receptor 4 signaling pathway / positive regulation of amyloid precursor protein catabolic process / regulation of platelet aggregation / negative regulation of immune response / B cell homeostasis / positive regulation of toll-like receptor 4 signaling pathway / dendritic cell differentiation / phosphorylation-dependent protein binding / positive regulation of toll-like receptor 9 signaling pathway / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Platelet Adhesion to exposed collagen / response to carbohydrate / CD22 mediated BCR regulation / histamine secretion by mast cell / gamma-tubulin binding / oligodendrocyte development / positive regulation of glial cell proliferation / regulation of release of sequestered calcium ion into cytosol / interleukin-5-mediated signaling pathway / regulation of cell adhesion mediated by integrin / platelet-derived growth factor receptor binding / Co-stimulation by CD28 / Fc epsilon receptor (FCERI) signaling / EPH-Ephrin signaling / B cell proliferation / postsynaptic specialization, intracellular component / leukocyte migration / Regulation of KIT signaling / regulation of erythrocyte differentiation / immunoglobulin receptor binding / EPHA-mediated growth cone collapse / negative regulation of MAP kinase activity / Co-inhibition by CTLA4 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / mitochondrial crista / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway / PECAM1 interactions / negative regulation of protein phosphorylation / hematopoietic progenitor cell differentiation / regulation of protein phosphorylation / response to axon injury / FCGR activation / response to amino acid / signaling receptor activator activity / growth hormone receptor signaling pathway via JAK-STAT / positive regulation of phosphorylation / EPH-ephrin mediated repulsion of cells / Role of LAT2/NTAL/LAB on calcium mobilization / lipopolysaccharide-mediated signaling pathway / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / fatty acid transport / Growth hormone receptor signaling / T cell costimulation / cellular response to retinoic acid / ephrin receptor binding / GPVI-mediated activation cascade / DNA damage checkpoint signaling / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / response to hormone / EPHB-mediated forward signaling / peptidyl-tyrosine phosphorylation / regulation of cytokine production / FCERI mediated Ca+2 mobilization / 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 / erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Cell surface interactions at the vascular wall
Similarity search - Function
Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
STAUROSPORINE / Tyrosine-protein kinase Lyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMiyano, N. / Kinoshita, T. / Tada, T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Structural basis for the inhibitor recognition of human Lyn kinase domain
Authors: Miyano, N. / Kinoshita, T. / Nakai, R. / Kirii, Y. / Yokota, K. / Tada, T.
History
DepositionJul 11, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Tyrosine-protein kinase Lyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4612
Polymers32,9951
Non-polymers4671
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.382, 128.382, 54.875
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Tyrosine-protein kinase Lyn


Mass: 32994.816 Da / Num. of mol.: 1 / Fragment: residues in UNP 233-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P07948, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 6212 / Num. obs: 5892
Reflection shellResolution: 3→3.14 Å

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DQ7

2dq7


Resolution: 3→50 Å / σ(F): 0
RfactorNum. reflection
Rfree0.324 -
Rwork0.293 -
all-6212
obs-5892
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 35 0 2112
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg2.1

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