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- PDB-1q6j: THE STRUCTURE OF PHOSPHOTYROSINE PHOSPHATASE 1B IN COMPLEX WITH C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q6j | |||||||||
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Title | THE STRUCTURE OF PHOSPHOTYROSINE PHOSPHATASE 1B IN COMPLEX WITH COMPOUND 2 | |||||||||
![]() | Protein-tyrosine phosphatase, non-receptor type 1 | |||||||||
![]() | HYDROLASE / PHOSPHATASE / SECONDARY BINDING SITE / SELECTIVITY | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Scapin, G. / Patel, S.B. / Becker, J.W. / Wang, Q. / Desponts, C. / Waddleton, D. / Skorey, K. / Cromlish, W. / Bayly, C. / Therien, M. ...Scapin, G. / Patel, S.B. / Becker, J.W. / Wang, Q. / Desponts, C. / Waddleton, D. / Skorey, K. / Cromlish, W. / Bayly, C. / Therien, M. / Gauthier, J.Y. / Li, C.S. / Lau, C.K. / Ramachandran, C. / Kennedy, B.P. / Asante-Appiah, E. | |||||||||
![]() | ![]() Title: The Structural Basis for the Selectivity of Benzotriazole Inhibitors of Ptp1B Authors: Scapin, G. / Patel, S.B. / Becker, J.W. / Wang, Q. / Desponts, C. / Waddleton, D. / Skorey, K. / Cromlish, W. / Bayly, C. / Therien, M. / Gauthier, J.Y. / Li, C.S. / Lau, C.K. / ...Authors: Scapin, G. / Patel, S.B. / Becker, J.W. / Wang, Q. / Desponts, C. / Waddleton, D. / Skorey, K. / Cromlish, W. / Bayly, C. / Therien, M. / Gauthier, J.Y. / Li, C.S. / Lau, C.K. / Ramachandran, C. / Kennedy, B.P. / Asante-Appiah, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.1 KB | Display | ![]() |
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PDB format | ![]() | 56.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1q6mC ![]() 1q6nC ![]() 1q6pC ![]() 1q6sC ![]() 1q6tC ![]() 1ptyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36238.172 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-335 / [ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.14 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 3350, MGCL2, HEPES, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRUKER / Detector: CCD / Date: Jun 11, 1999 |
Radiation | Monochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37 Å / Num. obs: 26132 / % possible obs: 93.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.084 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.2→1.34 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.404 / % possible all: 96 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 37 Å / Num. obs: 26131 / Redundancy: 8.7 % / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 93 % / Redundancy: 9 % / Num. unique obs: 4348 / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PTY Resolution: 2.2→25 Å / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: MASK / Bsol: 33.63 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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