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Yorodumi- PDB-3wkc: Crystal structure of soluble epoxide hydrolase in complex with fr... -
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-Basic information
Entry | Database: PDB / ID: 3wkc | ||||||
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Title | Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor | ||||||
Components | Bifunctional epoxide hydrolase 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Hydrolase / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Amano, Y. / Yamaguchi, T. / Tanabe, E. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2014 Title: Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography. Authors: Amano, Y. / Yamaguchi, T. / Tanabe, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wkc.cif.gz | 118.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wkc.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/3wkc ftp://data.pdbj.org/pub/pdb/validation_reports/wk/3wkc | HTTPS FTP |
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-Related structure data
Related structure data | 3wk4C 3wk5C 3wk6C 3wk7C 3wk8C 3wk9C 3wkaC 3wkbC 3wkdC 3wkeC C: citing same article (ref.) |
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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: 63514.512 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, lipid-phosphate phosphatase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-S0J / |
#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: 2.37 Å3/Da / Density % sol: 48.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Potassium phosphate, 0.2M Ammonium dihydrogen phosphate, 25%w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→46.26 Å / Num. obs: 30416 / % possible obs: 99.4 % |
Reflection shell | Resolution: 2.2→2.257 Å / % possible all: 96.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.548 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.213 / 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: 33.553 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→46.26 Å
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Refine LS restraints |
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