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- PDB-4y2v: Structure of soluble epoxide hydrolase in complex with (4-bromo-3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4y2v | ||||||
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Title | Structure of soluble epoxide hydrolase in complex with (4-bromo-3-cyclopropyl-1H-pyrazol-1-yl)acetic acid | ||||||
![]() | Bifunctional epoxide hydrolase 2 | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / hydrolase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / phospholipid dephosphorylation / 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 / soluble epoxide hydrolase / phospholipid dephosphorylation / 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 / dephosphorylation / phosphatase activity / peroxisomal matrix / toxic substance binding / 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 | ![]() | 122.2 KB | Display | ![]() |
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PDB format | ![]() | 93.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4y2jC ![]() 4y2pC ![]() 4y2qC ![]() 4y2rC ![]() 4y2sC ![]() 4y2tC ![]() 4y2uC ![]() 4y2xC ![]() 4y2yC ![]() 1s8oS C: citing same article ( S: Starting model for refinement |
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-4A5 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.88 % |
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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: 2.4→100 Å / Num. obs: 24672 / % possible obs: 98.8 % / Redundancy: 6.9 % / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 4.6 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1S8O Resolution: 2.4→79.85 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.516 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 29.087 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→79.85 Å
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Refine LS restraints |
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