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Yorodumi- PDB-1g1h: CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g1h | ||||||
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Title | CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH A BIS-PHOSPHORYLATED PEPTIDE (ETD(PTR)(PTR)RKGGKGLL) FROM THE INSULIN RECEPTOR KINASE | ||||||
Components |
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Keywords | HYDROLASE / SIGNALING PROTEIN / HYDROLASE (PHOSPHORYLATION) / TYROSINE PHOSPHATASE / PEPTIDE 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 / Resolution: 2.4 Å | ||||||
Authors | Salmeen, A. / Andersen, J.N. / Myers, M.P. / Tonks, N.K. / Barford, D. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: Molecular basis for the dephosphorylation of the activation segment of the insulin receptor by protein tyrosine phosphatase 1B. Authors: Salmeen, A. / Andersen, J.N. / Myers, M.P. / Tonks, N.K. / Barford, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g1h.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g1h.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 1g1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g1h_validation.pdf.gz | 428.6 KB | Display | wwPDB validaton report |
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Full document | 1g1h_full_validation.pdf.gz | 429.6 KB | Display | |
Data in XML | 1g1h_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 1g1h_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/1g1h ftp://data.pdbj.org/pub/pdb/validation_reports/g1/1g1h | HTTPS FTP |
-Related 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: 34688.504 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: C215A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-19B / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase |
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#2: Protein/peptide | Mass: 1662.651 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Sequence from the activation segment of the Insulin Recptor Kinase |
#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: 2.94 Å3/Da / Density % sol: 58.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 302 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, MgCl2, dithiothreitol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 302.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 17, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 16411 / Num. obs: 16411 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.3 |
Reflection shell | Highest resolution: 2.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.132 / Num. unique all: 1601 / % possible all: 96 |
Reflection | *PLUS Num. measured all: 105145 |
Reflection shell | *PLUS % possible obs: 96 % |
-Processing
Software |
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Refinement | Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.207 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 2.5 |