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Open data
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Basic information
Entry | Database: PDB / ID: 1sug | ||||||
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Title | 1.95 A structure of apo protein tyrosine phosphatase 1B | ||||||
![]() | Protein-tyrosine phosphatase, non-receptor type 1 | ||||||
![]() | HYDROLASE / WPD-loop closed / water molecule network | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Pedersen, A.K. / Peters, G.H. / Moller, K.B. / Iversen, L.F. / Kastrup, J.S. | ||||||
![]() | ![]() Title: Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B. Authors: Pedersen, A.K. / Peters G, G.H. / Moller, K.B. / Iversen, L.F. / Kastrup, J.S. #1: ![]() Title: Crystal structure of human protein tyrosine phosphatase 1B Authors: Barford, D. / Flint, A.J. / Tonks, N.K. #2: Journal: J.Chromatogr.,B / Year: 2004 Title: Affinity purification of recombinant protein-tyrosine phosphatase 1B using a highly selective inhibitor Authors: Pedersen, A.K. / Branner, S. / Mortensen, S.B. / Andersen, H.S. / Klausen, K.M. / Moller, K.B. / Moller, N.P. / Iversen, L.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.8 KB | Display | ![]() |
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PDB format | ![]() | 59.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1c83S 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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Details | The asymmetric unit of the crystal contains one molecule corresponding to the biologically active form |
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Components
#1: Protein | Mass: 37365.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-TRS / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, magnesium acetate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 28, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45 Å / Num. all: 34528 / Num. obs: 34528 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3375 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1c83 Resolution: 1.95→45 Å / Isotropic thermal model: anisotropic / Cross valid method: Troughout / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The N-terminal methionine and the last 22 residues in the C-terminus could not be located in the electron density maps
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Displacement parameters | Biso mean: 28.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.015
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