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Yorodumi- PDB-3wka: Crystal structure of soluble epoxide hydrolase in complex with fr... -
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-Basic information
Entry | Database: PDB / ID: 3wka | ||||||
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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 / 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: 2.01 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 | 3wka.cif.gz | 121.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wka.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wka_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 3wka_full_validation.pdf.gz | 464.8 KB | Display | |
Data in XML | 3wka_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 3wka_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/3wka ftp://data.pdbj.org/pub/pdb/validation_reports/wk/3wka | HTTPS FTP |
-Related structure data
Related structure data | 3wk4C 3wk5C 3wk6C 3wk7C 3wk8C 3wk9C 3wkbC 3wkcC 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-S0G / |
#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: 2.35 Å3/Da / Density % sol: 47.75 % |
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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 source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 270 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→19.99 Å / Num. obs: 39143 / % possible obs: 98.75 % |
Reflection shell | Resolution: 2.01→2.062 Å / % possible all: 97.59 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→19.99 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.446 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.189 / 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: 25.946 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→19.99 Å
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Refine LS restraints |
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