+Open data
-Basic information
Entry | Database: PDB / ID: 6w30 | ||||||||||||
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Title | Protein Tyrosine Phosphatase 1B Bound to Amorphadiene | ||||||||||||
Components | Tyrosine-protein phosphatase non-receptor type 1 | ||||||||||||
Keywords | HYDROLASE / PTP1B / Allosteric Inhibitor / Terpenoid | ||||||||||||
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 / MECP2 regulates neuronal receptors and channels / Growth hormone receptor signaling / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Sarkar, A. / Kim, E.Y. / Hongdusit, A. / Sankaran, B. / Fox, J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Acs Synth Biol / Year: 2021 Title: Microbially Guided Discovery and Biosynthesis of Biologically Active Natural Products. Authors: Sarkar, A. / Kim, E.Y. / Jang, T. / Hongdusit, A. / Kim, H. / Choi, J.M. / Fox, J.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w30.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w30.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 6w30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w30_validation.pdf.gz | 934.4 KB | Display | wwPDB validaton report |
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Full document | 6w30_full_validation.pdf.gz | 936.8 KB | Display | |
Data in XML | 6w30_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 6w30_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/6w30 ftp://data.pdbj.org/pub/pdb/validation_reports/w3/6w30 | HTTPS FTP |
-Related structure data
Related structure data | 7lfoC 3a5jS S: Starting model for refinement 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: 38436.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P18031, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-SJA / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 66.06 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 140 g/L PEG8000, 100 mM HEPES, 200 mM magnesium acetate, pH 7.5 Temp details: Crystals were seeded and grown at 277.15 K. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00003 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2019 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→62.34 Å / Num. obs: 28751 / % possible obs: 99.8 % / Redundancy: 10.7 % / Biso Wilson estimate: 35.2 Å2 / CC1/2: 0.985 / Χ2: 32.58 / Net I/σ(I): 0.442 |
Reflection shell | Resolution: 2.1→2.13 Å / Redundancy: 5.6 % / Num. unique obs: 1314 / CC1/2: 0.324 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3A5J Resolution: 2.1→44.52 Å / SU ML: 0.2525 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.1361 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.52 Å
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Refine LS restraints |
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LS refinement shell |
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