+Open data
-Basic information
Entry | Database: PDB / ID: 1g7f | ||||||
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Title | HUMAN PTP1B CATALYTIC DOMAIN COMPLEXED WITH PNU177496 | ||||||
Components | PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 | ||||||
Keywords | HYDROLASE / HYDROLASE (PHOSPHORYLATION) / TYROSINE PHOSPHATASE / INHIBITOR / COMPLEX | ||||||
Function / homology | Function and homology information 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 MAP kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bleasdale, J.E. / Ogg, D. / Larsen, S.D. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Small molecule peptidomimetics containing a novel phosphotyrosine bioisostere inhibit protein tyrosine phosphatase 1B and augment insulin action. Authors: Bleasdale, J.E. / Ogg, D. / Palazuk, B.J. / Jacob, C.S. / Swanson, M.L. / Wang, X.Y. / Thompson, D.P. / Conradi, R.A. / Mathews, W.R. / Laborde, A.L. / Stuchly, C.W. / Heijbel, A. / ...Authors: Bleasdale, J.E. / Ogg, D. / Palazuk, B.J. / Jacob, C.S. / Swanson, M.L. / Wang, X.Y. / Thompson, D.P. / Conradi, R.A. / Mathews, W.R. / Laborde, A.L. / Stuchly, C.W. / Heijbel, A. / Bergdahl, K. / Bannow, C.A. / Smith, C.W. / Svensson, C. / Liljebris, C. / Schostarez, H.J. / May, P.D. / Stevens, F.C. / Larsen, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g7f.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g7f.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 1g7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g7f_validation.pdf.gz | 714.5 KB | Display | wwPDB validaton report |
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Full document | 1g7f_full_validation.pdf.gz | 720.1 KB | Display | |
Data in XML | 1g7f_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 1g7f_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/1g7f ftp://data.pdbj.org/pub/pdb/validation_reports/g7/1g7f | HTTPS FTP |
-Related structure data
Related structure data | 1g7gC 1ptvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34706.539 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN (RESIDUES 1-298) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-INZ / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG8000, magnesium acetate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9765 Å |
Detector | Type: SIEMENS / Detector: CCD / Date: Oct 27, 1997 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 37591 / Num. obs: 36586 / % possible obs: 97.33 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.79 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.74 % / Rmerge(I) obs: 0.348 / % possible all: 97.33 |
Reflection | *PLUS Num. measured all: 643419 |
Reflection shell | *PLUS % possible obs: 97 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ptv Resolution: 1.8→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / σ(F): 0 / Rfactor Rwork: 0.18 | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |