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- PDB-4y2p: Structure of soluble epoxide hydrolase in complex with N-methyl-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4y2p | ||||||
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Title | Structure of soluble epoxide hydrolase in complex with N-methyl-1-[3-(pyridin-3-yl)phenyl]methanamine | ||||||
![]() | Bifunctional epoxide hydrolase 2 | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor complex / hydrolase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / Biosynthesis of maresins / phospholipid dephosphorylation / soluble epoxide hydrolase / epoxide metabolic process / lipid phosphatase activity / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) ...lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / Biosynthesis of maresins / phospholipid dephosphorylation / soluble epoxide hydrolase / epoxide metabolic process / lipid phosphatase activity / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / dephosphorylation / cholesterol homeostasis / Peroxisomal protein import / response to toxic substance / peroxisome / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Amano, Y. / Yamaguchi, T. | ||||||
![]() | ![]() Title: Identification of N-ethylmethylamine as a novel scaffold for inhibitors of soluble epoxide hydrolase by crystallographic fragment screening Authors: Amano, Y. / Tanabe, E. / Yamaguchi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.3 KB | Display | ![]() |
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PDB format | ![]() | 95.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.9 KB | Display | ![]() |
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Full document | ![]() | 454.6 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y2jC ![]() 4y2qC ![]() 4y2rC ![]() 4y2sC ![]() 4y2tC ![]() 4y2uC ![]() 4y2vC ![]() 4y2xC ![]() 4y2yC 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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Unit cell |
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Components
#1: Protein | Mass: 63514.512 Da / Num. of mol.: 1 / Fragment: UNP residues 1-555 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-3C5 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Potassium phosphate, Ammonium dihydrogen phosphate, PEG3350 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 31, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→80.59 Å / Num. obs: 39866 / % possible obs: 98.8 % / Redundancy: 7.1 % / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.9 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 30.944 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→80.59 Å
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Refine LS restraints |
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