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- PDB-4rhg: Crystal structure of PTPN3 (PTPH1) D811E, C842S mutant in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rhg | ||||||
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Title | Crystal structure of PTPN3 (PTPH1) D811E, C842S mutant in complex with Eps15 pTyr849 peptide | ||||||
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![]() | HYDROLASE/PROTEIN BINDING / Alpha Beta / Hydrolase / HYDROLASE-PROTEIN BINDING complex | ||||||
Function / homology | ![]() regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / Golgi to endosome transport / regulation of sodium ion transmembrane transporter activity / clathrin coat of coated pit / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / endocytic recycling / aggresome ...regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / Golgi to endosome transport / regulation of sodium ion transmembrane transporter activity / clathrin coat of coated pit / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / endocytic recycling / aggresome / endosomal transport / positive regulation of receptor recycling / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / polyubiquitin modification-dependent protein binding / sodium channel regulator activity / clathrin-coated pit / cytoskeletal protein binding / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / protein tyrosine phosphatase activity / liver regeneration / EGFR downregulation / Negative regulation of MET activity / cytoplasmic side of plasma membrane / SH3 domain binding / endocytosis / Negative regulation of MAPK pathway / MAPK cascade / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / regulation of cell population proliferation / early endosome membrane / ATPase binding / postsynapse / receptor-mediated endocytosis of virus by host cell / cytoskeleton / symbiont entry into host cell / cadherin binding / apical plasma membrane / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, K.-E. / Meng, T.C. / Wang, A.H.-J. | ||||||
![]() | ![]() Title: Substrate specificity and plasticity of FERM-containing protein tyrosine phosphatases. Authors: Chen, K.E. / Li, M.Y. / Chou, C.C. / Ho, M.R. / Chen, G.C. / Meng, T.C. / Wang, A.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.2 KB | Display | ![]() |
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PDB format | ![]() | 100.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 301.9 KB | Display | ![]() |
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Full document | ![]() | 304.1 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rh5SC ![]() 4rh9C ![]() 4ri4C ![]() 4ri5C ![]() 4s0gC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34945.695 Da / Num. of mol.: 1 / Fragment: Catalytic domain (UNP RESIDUES 628-909) / Mutation: D811E, C842S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1124.005 Da / Num. of mol.: 1 / Fragment: pTyr849 peptide (UNP RESIDUES 846-854) / Source method: obtained synthetically / Details: Synthetic construct / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl, 21% PEG 8000, 5% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 16, 2013 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→30 Å / Num. all: 37336 / Num. obs: 37336 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 39.8 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 8.9 / Num. unique all: 3785 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4RH5 Resolution: 1.581→26.851 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 21.52 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.581→26.851 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: 13
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