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- PDB-4ge5: Crystal structure of human protein tyrosine phosphatase PTPN9 (ME... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ge5 | ||||||
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Title | Crystal structure of human protein tyrosine phosphatase PTPN9 (MEG2) complex with compound 5 | ||||||
![]() | Tyrosine-protein phosphatase non-receptor type 9 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() neuron projection terminus / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / positive regulation of protein localization to plasma membrane / negative regulation of neuron projection development / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Z.-Y. / Liu, S. / Zhang, S. | ||||||
![]() | ![]() Title: A Highly Selective and Potent PTP-MEG2 Inhibitor with Therapeutic Potential for Type 2 Diabetes. Authors: Zhang, S. / Liu, S. / Tao, R. / Wei, D. / Chen, L. / Shen, W. / Yu, Z.H. / Wang, L. / Jones, D.R. / Dong, X.C. / Zhang, Z.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.7 KB | Display | ![]() |
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PDB format | ![]() | 108.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777.7 KB | Display | ![]() |
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Full document | ![]() | 790.3 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ge2SC ![]() 4ge6C 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36229.055 Da / Num. of mol.: 2 Fragment: tyrosine-protein phosphatase domain (UNP residues 277-582) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain (production host): phage-resistant derivative of BL21(DE3) References: UniProt: P43378, protein-tyrosine-phosphatase #2: Chemical | ChemComp-A89 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 25% PEG3350, 0.2 M potassium thiocyanate, 10% ethylene glycol, 0.1 M Bis-Tris propane, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 210r / Detector: CCD |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 52574 / % possible obs: 95.6 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.083 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4GE2 Resolution: 2→50 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1218 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 52.9605 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 75.94 Å2 / Biso mean: 27.8934 Å2 / Biso min: 9.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Xplor file |
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