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Yorodumi- PDB-2lk4: Structural and mechanistic insights into the interaction between ... -
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-Basic information
Entry | Database: PDB / ID: 2lk4 | ||||||
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Title | Structural and mechanistic insights into the interaction between PAT Pyk2 and Paxillin LD motif | ||||||
Components | Protein-tyrosine kinase 2-beta | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / regulation of postsynaptic density assembly / blood vessel endothelial cell migration ...regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / regulation of postsynaptic density assembly / blood vessel endothelial cell migration / negative regulation of muscle cell apoptotic process / negative regulation of bone mineralization / cortical cytoskeleton organization / apical dendrite / positive regulation of ubiquitin-dependent protein catabolic process / regulation of release of sequestered calcium ion into cytosol / activation of Janus kinase activity / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Interleukin-2 signaling / sprouting angiogenesis / oocyte maturation / long-term synaptic depression / regulation of NMDA receptor activity / calmodulin-dependent protein kinase activity / Signal regulatory protein family interactions / positive regulation of cell-matrix adhesion / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of actin filament polymerization / stress fiber assembly / negative regulation of potassium ion transport / positive regulation of excitatory postsynaptic potential / RHOU GTPase cycle / response to immobilization stress / positive regulation of protein kinase activity / postsynaptic density, intracellular component / glial cell proliferation / cellular defense response / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / response to glucose / response to mechanical stimulus / cellular response to retinoic acid / peptidyl-tyrosine autophosphorylation / bone resorption / response to cAMP / tumor necrosis factor-mediated signaling pathway / ionotropic glutamate receptor signaling pathway / positive regulation of endothelial cell migration / positive regulation of synaptic transmission, glutamatergic / response to cocaine / response to hormone / positive regulation of translation / integrin-mediated signaling pathway / response to ischemia / long-term synaptic potentiation / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / response to calcium ion / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / : / neuron projection development / positive regulation of nitric oxide biosynthetic process / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / presynapse / lamellipodium / cell cortex / cell body / regulation of cell shape / positive regulation of cytosolic calcium ion concentration / growth cone / positive regulation of cell growth / protein-containing complex assembly / protein tyrosine kinase activity / response to ethanol / adaptive immune response / negative regulation of neuron apoptotic process / dendritic spine / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / cytoskeleton Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Model details | minimized average structure, model 1 | ||||||
Model type details | minimized average | ||||||
Authors | Vanarotti, M. / Miller, D. / Guibao, C. / Zheng, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Structural and Mechanistic Insights into the Interaction between Pyk2 and Paxillin LD Motifs. Authors: Vanarotti, M.S. / Miller, D.J. / Guibao, C.D. / Nourse, A. / Zheng, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lk4.cif.gz | 943.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lk4.ent.gz | 815.5 KB | Display | PDB format |
PDBx/mmJSON format | 2lk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/2lk4 ftp://data.pdbj.org/pub/pdb/validation_reports/lk/2lk4 | HTTPS FTP |
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-Related 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: 14815.045 Da / Num. of mol.: 1 Fragment: Focal adhesion targeting (FAT) region residues 871-1005 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2B, FAK2, PYK2, RAFTK / Production host: Escherichia coli (E. coli) References: UniProt: Q14289, non-specific protein-tyrosine kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5-1 mM [U-100% 13C; U-100% 15N] MES, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Units: mM / Component: MES-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] / Conc. range: 0.5-1 |
Sample conditions | Ionic strength: 7 / pH: 6.2 / Pressure: ambient / Temperature: 305 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: minimized average structure | |||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 100 / Conformers submitted total number: 20 |