+Open data
-Basic information
Entry | Database: PDB / ID: 2zn7 | ||||||
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Title | CRYSTAL STRUCTURES OF PTP1B-Inhibitor Complexes | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 1 | ||||||
Keywords | HYDROLASE / PTP1B / protein-inhibitor complex / Acetylation / Endoplasmic reticulum / Membrane / Oxidation / Phosphoprotein / Polymorphism / Protein phosphatase | ||||||
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 / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / 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 / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / positive regulation of protein tyrosine kinase activity / 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 insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / protein phosphatase 2A binding / negative regulation of MAP kinase activity / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Xu, W. / Wu, J. | ||||||
Citation | Journal: Chemmedchem / Year: 2008 Title: Structure-based optimization of protein tyrosine phosphatase-1 B inhibitors: capturing interactions with arginine 24 Authors: Wan, Z.-K. / Lee, J. / Hotchandani, R. / Moretto, A. / Binnun, E. / Wilson, D.P. / Kirincich, S.J. / Follows, B.C. / Ipek, M. / Xu, W. / Joseph-McCarthy, D. / Zhang, Y.-L. / Tam, M. / Erbe, ...Authors: Wan, Z.-K. / Lee, J. / Hotchandani, R. / Moretto, A. / Binnun, E. / Wilson, D.P. / Kirincich, S.J. / Follows, B.C. / Ipek, M. / Xu, W. / Joseph-McCarthy, D. / Zhang, Y.-L. / Tam, M. / Erbe, D.V. / Tobin, J.F. / Li, W. / Tam, S.Y. / Mansour, T.S. / Wu, J. | ||||||
History |
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Remark 40 | MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ... MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zn7.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zn7.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/2zn7 ftp://data.pdbj.org/pub/pdb/validation_reports/zn/2zn7 | HTTPS FTP |
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-Related structure data
Related structure data | 2zmmC 2qbqS 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: 34833.723 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTP1B / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-410 / |
#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: 3.4 Å3/Da / Density % sol: 63.88 % |
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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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 27, 2003 |
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: 28183 / Num. obs: 27588 / % possible obs: 97.89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.98 Å2 / Rmerge(I) obs: 0.077 |
Reflection shell | Resolution: 2.1→2.17 Å / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 6.88 / Num. unique all: 2915 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QBQ Resolution: 2.1→19.7 Å / FOM work R set: 0.88 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 49.69 Å2 / ksol: 0.381 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 6.6 Å2 / Biso mean: 26.32 Å2 / Biso min: 79.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.7 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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