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Open data
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Basic information
Entry | Database: PDB / ID: 6b8t | ||||||
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Title | Multiconformer model of apo WT PTP1B with glycerol at 240 K | ||||||
![]() | Tyrosine-protein phosphatase non-receptor type 1 | ||||||
![]() | SIGNALING PROTEIN / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / multitemperature / multiconformer | ||||||
Function / homology | ![]() regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / positive regulation of receptor catabolic process / insulin receptor recycling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane ...regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / positive regulation of receptor catabolic process / insulin receptor recycling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / 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 / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / MECP2 regulates neuronal receptors and channels / Growth hormone receptor signaling / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / 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 / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Keedy, D.A. / Hill, Z.B. / Biel, J.T. / Kang, E. / Rettenmaier, T.J. / Brandao-Neto, J. / von Delft, F. / Wells, J.A. / Fraser, J.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. Authors: Keedy, D.A. / Hill, Z.B. / Biel, J.T. / Kang, E. / Rettenmaier, T.J. / Brandao-Neto, J. / Pearce, N.M. / von Delft, F. / Wells, J.A. / Fraser, J.S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.4 KB | Display | ![]() |
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PDB format | ![]() | 121.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5qdeC ![]() 5qdfC ![]() 5qdgC ![]() 5qdhC ![]() 5qdiC ![]() 5qdjC ![]() 5qdkC ![]() 5qdlC ![]() 5qdmC ![]() 5qdnC ![]() 5qdoC ![]() 5qdpC ![]() 5qdqC ![]() 5qdrC ![]() 5qdsC ![]() 5qdtC ![]() 5qduC ![]() 5qdvC ![]() 5qdwC ![]() 5qdxC ![]() 5qdyC ![]() 5qdzC ![]() 5qe0C ![]() 5qe1C ![]() 5qe2C ![]() 5qe3C ![]() 5qe4C ![]() 5qe5C ![]() 5qe6C ![]() 5qe7C ![]() 5qe8C ![]() 5qe9C ![]() 5qeaC ![]() 5qebC ![]() 5qecC ![]() 5qedC ![]() 5qeeC ![]() 5qefC ![]() 5qegC ![]() 5qehC ![]() 5qeiC ![]() 5qejC ![]() 5qekC ![]() 5qelC ![]() 5qemC ![]() 5qenC ![]() 5qeoC ![]() 5qepC ![]() 5qeqC ![]() 5qerC ![]() 5qesC ![]() 5qetC ![]() 5qeuC ![]() 5qevC ![]() 5qewC ![]() 5qexC ![]() 5qeyC ![]() 5qezC ![]() 5qf0C ![]() 5qf1C ![]() 5qf2C ![]() 5qf3C ![]() 5qf4C ![]() 5qf5C ![]() 5qf6C ![]() 5qf7C ![]() 5qf8C ![]() 5qf9C ![]() 5qfaC ![]() 5qfbC ![]() 5qfcC ![]() 5qfdC ![]() 5qfeC ![]() 5qffC ![]() 5qfgC ![]() 5qfhC ![]() 5qfiC ![]() 5qfjC ![]() 5qfkC ![]() 5qflC ![]() 5qfmC ![]() 5qfnC ![]() 5qfoC ![]() 5qfpC ![]() 5qfqC ![]() 5qfrC ![]() 5qfsC ![]() 5qftC ![]() 5qfuC ![]() 5qfvC ![]() 5qfwC ![]() 5qfxC ![]() 5qfyC ![]() 5qfzC ![]() 5qg0C ![]() 5qg1C ![]() 5qg2C ![]() 5qg3C ![]() 5qg4C ![]() 5qg5C ![]() 5qg6C ![]() 5qg7C ![]() 5qg8C ![]() 5qg9C ![]() 5qgaC ![]() 5qgbC ![]() 5qgcC ![]() 5qgdC ![]() 5qgeC ![]() 5qgfC ![]() 6b8eC ![]() 6b8xC ![]() 6b8zC ![]() 6b90C ![]() 6b95C ![]() 6baiC C: citing same article ( |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37345.562 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: C32S, C92V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 16% PEG 8000, 2% ethanol, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 240 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.115869 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→62.54 Å / Num. obs: 42343 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.062 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.085 / Χ2: 1.024 / Net I/σ(I): 15.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.99 Å2 / Biso mean: 40.1592 Å2 / Biso min: 13.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→62.54 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %
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