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Yorodumi- PDB-4od0: Crystal structure of human soluble epoxide hydrolase complexed wi... -
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-Basic information
Entry | Database: PDB / ID: 4od0 | ||||||
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Title | Crystal structure of human soluble epoxide hydrolase complexed with 1-(1-propanoylpiperidin-4-yl)-3-[4-(trifluoromethoxy)phenyl]urea | ||||||
Components | Bifunctional epoxide hydrolase 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / domain-swapped dimer / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / Biosynthesis of maresins / soluble epoxide hydrolase / epoxide metabolic process / 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 / Biosynthesis of maresins / soluble epoxide hydrolase / epoxide metabolic process / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å | ||||||
Authors | Lee, K.S.S. / Liu, J. / Wagner, K.M. / Pakhomova, S. / Dong, H. / Morisseau, C. / Fu, S.H. / Yang, J. / Wang, P. / Ulu, A. ...Lee, K.S.S. / Liu, J. / Wagner, K.M. / Pakhomova, S. / Dong, H. / Morisseau, 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. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4od0.cif.gz | 227.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4od0.ent.gz | 183.3 KB | Display | PDB format |
PDBx/mmJSON format | 4od0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4od0_validation.pdf.gz | 658.6 KB | Display | wwPDB validaton report |
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Full document | 4od0_full_validation.pdf.gz | 667.7 KB | Display | |
Data in XML | 4od0_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 4od0_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/4od0 ftp://data.pdbj.org/pub/pdb/validation_reports/od/4od0 | HTTPS FTP |
-Related structure data
Related structure data | 4oczC 1s8oS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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 / Plasmid: ACHSEH1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-2RV / |
#5: 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: 2.38 Å3/Da / Density % sol: 48.28 % |
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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: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38079 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 21, 2011 / Details: MIRRORS |
Radiation | Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38079 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→40 Å / Num. all: 14096 / Num. obs: 14096 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 82.1 Å2 / Rsym value: 0.111 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.92→3.02 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1360 / Rsym value: 0.745 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S8O Resolution: 2.92→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.91 / SU B: 36.763 / SU ML: 0.322 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.429 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.396 Å2
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Refinement step | Cycle: LAST / Resolution: 2.92→40 Å
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Refine LS restraints |
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