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- PDB-1een: CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1een | ||||||
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Title | CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH ACETYL-D-A-D-BPA-PTYR-L-I-P-Q-Q-G | ||||||
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![]() | HYDROLASE / ACETYLATION / PHOSPHORYLATION / INHIBITION | ||||||
Function / homology | ![]() regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / 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 / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / 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 / Growth hormone receptor signaling / MECP2 regulates neuronal receptors and channels / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Puius, Y.A. / Zhao, Y. / Almo, S.C. / Zhang, Z.Y. | ||||||
![]() | ![]() Title: Structural basis of plasticity in protein tyrosine phosphatase 1B substrate recognition. Authors: Sarmiento, M. / Puius, Y.A. / Vetter, S.W. / Keng, Y.F. / Wu, L. / Zhao, Y. / Lawrence, D.S. / Almo, S.C. / Zhang, Z.Y. #1: ![]() Title: Assessment of Protein-Tyrosine Phosphatase 1B Specificity Using "Inverse Alanine Scanning" Authors: Vetter, S.W. / Keng, Y.F. / Lawrence, D.S. / Zhang, Z.Y. #2: ![]() Title: Molecular Basis of Substrate Specificity of Protein-Tyrosine Phosphatase 1B Authors: Sarmiento, M. / Zhao, Y. / Gordon, S.J. / Zhang, Z.Y. #3: ![]() Title: Determinants of Substrate Recognition in the Protein Tyrosine Phosphatase, Ptp1 Authors: Zhang, Z.Y. / Walsh, A.B. / Wu, L. / Mcnamara, D.J. / Dobrusin, E.M. / Miller, W.T. #4: ![]() Title: Identification of a Second Aryl Phosphate-Binding Site in Protein-Tyrosine Phosphatase 1B: A Paradigm for Inhibitor Design Authors: Puius, Y.A. / Zhao, Y. / Sullivan, M. / Lawrence, D.S. / Almo, S.C. / Zhang, Z.Y. #5: ![]() Title: Structural Basis for Phosphotyrosine Peptide Recognition by Protein Tyrosine Phosphatase 1B Authors: Jia, Z. / Barford, D. / Flint, A.J. / Tonks, N.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.8 KB | Display | ![]() |
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PDB format | ![]() | 62.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387.9 KB | Display | ![]() |
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Full document | ![]() | 391.5 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1eeoC ![]() 1aaxS 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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Unit cell |
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Components
#1: Protein | Mass: 37349.574 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-321 / Mutation: C215S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 1022.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: May 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→90 Å / Num. obs: 32272 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 4.8 / % possible all: 63.7 |
Reflection | *PLUS Num. measured all: 160542 |
Reflection shell | *PLUS % possible obs: 63.7 % / Num. unique obs: 2160 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AAX Resolution: 1.9→19.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 414834.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: ONLY 8 OUT OF TWELVE PEPTIDE RESIDUES ARE VISIBLE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.02 Å2 / ksol: 0.403 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.364 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.282 / Rfactor obs: 0.282 |