+Open data
-Basic information
Entry | Database: PDB / ID: 2f6w | ||||||
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Title | Protein tyrosine phosphatase 1B with sulfamic acid inhibitors | ||||||
Components | Tyrosine-protein phosphatase, non-receptor type 1 | ||||||
Keywords | HYDROLASE / PTP1B / sulfamic acids / tetrahydroisoquinoline / phosphatase / tyrosine | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Evdokimov, A.G. / Pokross, M.E. / Klopfenstein, S.R. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: 1,2,3,4-Tetrahydroisoquinolinyl sulfamic acids as phosphatase PTP1B inhibitors Authors: Klopfenstein, S.R. / Evdokimov, A.G. / Colson, A.-O. / Fairweather, N.T. / Neuman, J.J. / Maier, M.B. / Gray, J.L. / Gerwe, G.S. / Stake, G.E. / Howard, B.W. / Farmer, J.A. / Pokross, M.E. / ...Authors: Klopfenstein, S.R. / Evdokimov, A.G. / Colson, A.-O. / Fairweather, N.T. / Neuman, J.J. / Maier, M.B. / Gray, J.L. / Gerwe, G.S. / Stake, G.E. / Howard, B.W. / Farmer, J.A. / Pokross, M.E. / Downs, T.R. / Kasibhatla, B. / Peters, K.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f6w.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f6w.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 2f6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f6w_validation.pdf.gz | 740.7 KB | Display | wwPDB validaton report |
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Full document | 2f6w_full_validation.pdf.gz | 746.1 KB | Display | |
Data in XML | 2f6w_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2f6w_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/2f6w ftp://data.pdbj.org/pub/pdb/validation_reports/f6/2f6w | HTTPS FTP |
-Related structure data
Related structure data | 2f6tC 2f6vC 2f6yC 2f6zC 2f70C 2f71C 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: 34720.566 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) / Gene: PTPN1, PTP1B / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-UN3 / ( | #5: 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: 3.34 Å3/Da / Density % sol: 63.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 18% PEG4000, 200 mM MgCl2, 100 mM TRIS-HCl, pH 8.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å | |||||||||
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Mar 3, 2001 / Details: Montel | |||||||||
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 2.2→30.7 Å / Num. all: 22552 / Num. obs: 22552 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.83 | |||||||||
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.36 / Num. unique all: 2772 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PTV Resolution: 2.2→30.7 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.528 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.195 / ESU R Free: 0.192 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.223 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 43.8634 Å / Origin y: 16.8423 Å / Origin z: 2.2317 Å
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Refinement TLS group | Selection: ALL |