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- PDB-1oem: PTP1B with the catalytic cysteine oxidized to a sulfenyl-amide bond -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oem | ||||||
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Title | PTP1B with the catalytic cysteine oxidized to a sulfenyl-amide bond | ||||||
![]() | PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 | ||||||
![]() | HYDROLASE / PHOSPHORYLATION / PHOSPHATASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Salmeen, A. / Andersen, J.N. / Myers, M.P. / Meng, T.C. / Hinks, J.A. / Tonks, N.K. / Barford, D. | ||||||
![]() | ![]() Title: Redox Regulation of Protein Tyrosine Phosphatase Involves a Sulfenyl-Amide Intermediate Authors: Salmeen, A. / Andersen, J.N. / Myers, M.P. / Meng, T.C. / Hinks, J.A. / Tonks, N.K. / Barford, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 75.5 KB | Display | ![]() |
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PDB format | ![]() | 55.2 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1oeoC ![]() 2hnpS 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: 37365.637 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-321 Source method: isolated from a genetically manipulated source Details: SULFENYL-AMIDE BOND BETWEEN CYS215 SG AND SER216 N / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Compound details | CATALYSES THE HYDROLYSIS OF PROTEIN TYROSINE PHOSPHATE TO PROTEIN TYROSINE AND PHOSPHATE.BELONGS TO ...CATALYSES THE HYDROLYSIS |
Sequence details | MODRES: 1OEM CYS X 215() MODIFIED CYSTEINE, OXIDATION TO A SULFENYL AMIDE BOND BETWEEN CYS 215, SER ...MODRES: 1OEM CYS X 215() MODIFIED CYSTEINE, OXIDATION TO A SULFENYL AMIDE BOND BETWEEN CYS 215, SER 216 MODRES: 1OEM SER X 216() MODIFIED SERINE, FORMS A SULFENYL AMIDE BOND WITH CYS 215 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 66.75 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 0.1M HEPES PH 7.5, 12%PEG, 0.2M MGCL2. PROTEIN WAS OXIDIZED WITH A 1:1.25 MOLAR RATIO OF H2O2 - PROTEIN PRIOR TO CRYSTALLIZATION | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: unknown / Details: Barford, D., (1994) Science, 263, 1397. | |||||||||||||||||||||||||
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: ADSC CCD / Detector: CCD / Date: Jul 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 43606 / % possible obs: 99.5 % / Redundancy: 7.07 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 26.26 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 26.26 / % possible all: 99.3 |
Reflection | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 50 Å / Num. measured all: 308523 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.68 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HNP Resolution: 1.8→76.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.093 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: PROTEIN WAS OXIDIZED WITH A 1:1.25 MOLAR RATIO OF H2O2 PROTEIN PRIOR TO CRYSTALLIZATION
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→76.7 Å
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