+Open data
-Basic information
Entry | Database: PDB / ID: 3i1y | ||||||
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Title | Crystal Structure of soluble epoxide Hydrolase | ||||||
Components | Epoxide hydrolase 2 | ||||||
Keywords | HYDROLASE / Aromatic hydrocarbons catabolism / Cytoplasm / Detoxification / Magnesium / Metal-binding / Peroxisome / Polymorphism | ||||||
Function / homology | Function and homology information lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / epoxide metabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / 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 / phospholipid dephosphorylation / lipid phosphatase activity / epoxide metabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.469 Å | ||||||
Authors | Farrow, N.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Structure-based optimization of arylamides as inhibitors of soluble epoxide hydrolase. Authors: Eldrup, A.B. / Soleymanzadeh, F. / Taylor, S.J. / Muegge, I. / Farrow, N.A. / Joseph, D. / McKellop, K. / Man, C.C. / Kukulka, A. / De Lombaert, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i1y.cif.gz | 119 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i1y.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 3i1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/3i1y ftp://data.pdbj.org/pub/pdb/validation_reports/i1/3i1y | HTTPS FTP |
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-Related 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: 62685.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Escherichia coli (E. coli) / References: UniProt: P34913, soluble epoxide hydrolase |
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#2: Chemical | ChemComp-33N / |
#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: 2.41 Å3/Da / Density % sol: 48.96 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.469 Å / Num. obs: 23018 / Biso Wilson estimate: 48.07 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.469→38.096 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.765 / SU ML: 0.85 / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.368 Å2 / ksol: 0.344 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.23 Å2 / Biso mean: 52.717 Å2 / Biso min: 24.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.469→38.096 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: 8
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