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Yorodumi- PDB-1lqf: Structure of PTP1b in Complex with a Peptidic Bisphosphonate Inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lqf | ||||||
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Title | Structure of PTP1b in Complex with a Peptidic Bisphosphonate Inhibitor | ||||||
Components | protein-tyrosine phosphatase, non-receptor type 1 | ||||||
Keywords | HYDROLASE / Phosphatase / phosphonates / diabetes / inhibitor | ||||||
Function / homology | Function and homology information PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / positive regulation of protein tyrosine kinase activity / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / cellular response to unfolded protein / regulation of signal transduction / 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 / negative regulation of MAP kinase activity / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / protein dephosphorylation / Integrin signaling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein phosphatase 2A binding / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Asante-Appiah, E. / Patel, S. / Dufresne, C. / Scapin, G. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: The structure of PTP-1B in complex with a peptide inhibitor reveals an alternative binding mode for bisphosphonates. Authors: Asante-Appiah, E. / Patel, S. / Dufresne, C. / Roy, P. / Wang, Q. / Patel, V. / Friesen, R.W. / Ramachandran, C. / Becker, J.W. / Leblanc, Y. / Kennedy, B.P. / Scapin, G. #1: Journal: J.Biol.Chem. / Year: 2001 Title: The YRD motif is a major determinant of substrate and inhibitor specificity in T-cell protein-tyrosine phosphatase Authors: Asante-Appiah, E. / Ball, K. / Bateman, K. / Skorey, K. / Friesen, R. / Desponts, C. / Payette, P. / Bayly, C. / Zamboni, R. / Scapin, G. / Ramachandran, C. / Kennedy, B.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lqf.cif.gz | 255.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lqf.ent.gz | 206.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lqf_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1lqf_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1lqf_validation.xml.gz | 57.5 KB | Display | |
Data in CIF | 1lqf_validation.cif.gz | 76.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/1lqf ftp://data.pdbj.org/pub/pdb/validation_reports/lq/1lqf | HTTPS FTP |
-Related structure data
Related structure data | 1ptyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34451.367 Da / Num. of mol.: 4 / Fragment: catalytic domain (residues 1-283) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase #2: Chemical | ChemComp-BGD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 73 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: Peg 4000, propanol, citrate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 284K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 9, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29 Å / Num. all: 63052 / Num. obs: 61097 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 38.9 Å2 / Rsym value: 0.121 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 9039 / Rsym value: 0.38 / % possible all: 86.4 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 176274 / Rmerge(I) obs: 0.121 |
Reflection shell | *PLUS % possible obs: 86.4 % / Num. unique obs: 9039 / Num. measured obs: 17193 / Rmerge(I) obs: 0.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PTY Resolution: 2.5→29 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: A 4% twinning was detected using both Truncate and CNS and the refinement was carried out using the CNS twinning procedures, with twinning operator h, -k, -l.
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Displacement parameters | Biso mean: 42.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.68 Å / Total num. of bins used: 10
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 61052 / % reflection Rfree: 5 % / Rfactor obs: 0.231 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.228 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.438 / Rfactor Rwork: 0.366 |