+Open data
-Basic information
Entry | Database: PDB / ID: 2nta | ||||||
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Title | Crystal Structure of PTP1B-inhibitor Complex | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 1 | ||||||
Keywords | HYDROLASE / PTP1B / protein-inhibitor complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Xu, W. / Follows, B. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Probing acid replacements of thiophene PTP1B inhibitors. Authors: Wan, Z.K. / Follows, B. / Kirincich, S. / Wilson, D. / Binnun, E. / Xu, W. / Joseph-McCarthy, D. / Wu, J. / Smith, M. / Zhang, Y.L. / Tam, M. / Erbe, D. / Tam, S. / Saiah, E. / Lee, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nta.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nta.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 2nta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nta_validation.pdf.gz | 758.8 KB | Display | wwPDB validaton report |
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Full document | 2nta_full_validation.pdf.gz | 761.7 KB | Display | |
Data in XML | 2nta_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 2nta_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/2nta ftp://data.pdbj.org/pub/pdb/validation_reports/nt/2nta | HTTPS FTP |
-Related structure data
Related structure data | 2nt7C 2hce 2hcx 2hfa C: citing same article (ref.) |
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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: 34819.695 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-521 / |
#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: 3.36 Å3/Da / Density % sol: 63.42 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 17% PEG 4000, 0.15M MgCl2, 0.1M Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Aug 8, 2005 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 27925 / Num. obs: 27099 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.113 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.19 / Num. unique all: 2616 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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