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- PDB-4ocz: Crystal structure of human soluble epoxide hydrolase complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ocz | ||||||
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Title | Crystal structure of human soluble epoxide hydrolase complexed with 1-(1-isobutyrylpiperidin-4-yl)-3-(4-(trifluoromethyl)phenyl)urea | ||||||
![]() | Bifunctional epoxide hydrolase 2 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / domain-swapped dimer / HYDROLASE-HYDROLASE 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 | ![]() ![]() ![]() | ||||||
![]() | Lee, K.S.S. / Liu, J. / Wagner, K.M. / Pakhomova, S. / Dong, H. / Morriseau, C. / Fu, S.H. / Yang, J. / Wang, P. / Ulu, A. ...Lee, K.S.S. / Liu, J. / Wagner, K.M. / Pakhomova, S. / Dong, H. / Morriseau, C. / Fu, S.H. / Yang, J. / Wang, P. / Ulu, A. / Mate, C. / Nguyen, L. / Wullf, H. / Eldin, M.L. / Mara, A.A. / Newcomer, M.E. / Zeldin, D.C. / Hammock, B.D. | ||||||
![]() | ![]() Title: Optimized inhibitors of soluble epoxide hydrolase improve in vitro target residence time and in vivo efficacy. Authors: Lee, K.S. / Liu, J.Y. / Wagner, K.M. / Pakhomova, S. / Dong, H. / Morisseau, C. / Fu, S.H. / Yang, J. / Wang, P. / Ulu, A. / Mate, C.A. / Nguyen, L.V. / Hwang, S.H. / Edin, M.L. / Mara, A.A. ...Authors: Lee, K.S. / Liu, J.Y. / Wagner, K.M. / Pakhomova, S. / Dong, H. / Morisseau, C. / Fu, S.H. / Yang, J. / Wang, P. / Ulu, A. / Mate, C.A. / Nguyen, L.V. / Hwang, S.H. / Edin, M.L. / Mara, A.A. / Wulff, H. / Newcomer, M.E. / Zeldin, D.C. / Hammock, B.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.5 KB | Display | ![]() |
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PDB format | ![]() | 184.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 655 KB | Display | ![]() |
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Full document | ![]() | 669.3 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4od0C ![]() 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: 62685.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-2RU / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG3350, 0-10% sucrose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2012 |
Radiation | Monochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→75.89 Å / Num. all: 13582 / Num. obs: 13582 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 71 Å2 / Rsym value: 0.093 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.94→3.1 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1891 / Rsym value: 0.656 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1S8O Resolution: 2.94→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 46.981 / SU ML: 0.391 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 68.371 Å2
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Refinement step | Cycle: LAST / Resolution: 2.94→40 Å
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Refine LS restraints |
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