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- PDB-8exj: Crystal structure of PTP1B D181A/Q262A phosphatase domain in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8exj | ||||||
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Title | Crystal structure of PTP1B D181A/Q262A phosphatase domain in complex with a JAK1 activation loop phosphopeptide | ||||||
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![]() | SIGNALING PROTEIN / PTP1B / JAK/STAT / IRK | ||||||
Function / homology | ![]() protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / type III interferon-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of homotypic cell-cell adhesion / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway ...protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / type III interferon-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of homotypic cell-cell adhesion / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-2 signaling / growth hormone receptor binding / Other interleukin signaling / IFNG signaling activates MAPKs / regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / Interleukin-20 family signaling / interleukin-6-mediated signaling pathway / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / type I interferon-mediated signaling pathway / Interleukin-6 signaling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of sprouting angiogenesis / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / MAPK3 (ERK1) activation / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / Interleukin-10 signaling / MAPK1 (ERK2) activation / positive regulation of IRE1-mediated unfolded protein response / cell surface receptor signaling pathway via JAK-STAT / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / Growth hormone receptor signaling / MECP2 regulates neuronal receptors and channels / Signaling by CSF3 (G-CSF) / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / extrinsic component of cytoplasmic side of plasma membrane / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / Interleukin-7 signaling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / protein phosphatase 2A binding / protein tyrosine phosphatase activity / endosome lumen / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / insulin receptor binding / Negative regulation of MET activity / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / negative regulation of ERK1 and ERK2 cascade / cytoplasmic side of plasma membrane / receptor tyrosine kinase binding / cellular response to virus / ISG15 antiviral mechanism / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / Interferon gamma signaling / Interferon alpha/beta signaling / insulin receptor signaling pathway / actin cytoskeleton organization / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / cell differentiation / early endosome / cytoskeleton Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morris, R. / Kershaw, N.J. / Babon, J.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure guided studies of the interaction between PTP1B and JAK. Authors: Morris, R. / Keating, N. / Tan, C. / Chen, H. / Laktyushin, A. / Saiyed, T. / Liau, N.P.D. / Nicola, N.A. / Tiganis, T. / Kershaw, N.J. / Babon, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.6 KB | Display | ![]() |
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PDB format | ![]() | 56.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8exiC ![]() 8exkC ![]() 8exmC ![]() 8exnC ![]() 8eyaC ![]() 8eybC ![]() 8eycC ![]() 8f88C ![]() 1ptyS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34732.664 Da / Num. of mol.: 1 / Mutation: D181A/Q262A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 1920.033 Da / Num. of mol.: 1 / Fragment: residues 1027-1042 of JAK1 / Source method: obtained synthetically / Source: (synth.) ![]() References: UniProt: P23458, non-specific protein-tyrosine kinase | ||||
#3: Chemical | ChemComp-PO4 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.28 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, sitting drop Details: 12% Peg 4K, 0.1 M Calcium acetate, 0.05 M MES (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.301→45.503 Å / Num. obs: 24067 / % possible obs: 97.33 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1511 / Net I/σ(I): 9.56 |
Reflection shell | Resolution: 2.301→2.383 Å / Rmerge(I) obs: 4.248 / Num. unique obs: 2349 / CC1/2: 0.11 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PTY Resolution: 2.301→45.503 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.84 Å2 / Biso mean: 69.3133 Å2 / Biso min: 43.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.301→45.503 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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