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Yorodumi- PDB-4y2p: Structure of soluble epoxide hydrolase in complex with N-methyl-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y2p | ||||||
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Title | Structure of soluble epoxide hydrolase in complex with N-methyl-1-[3-(pyridin-3-yl)phenyl]methanamine | ||||||
Components | Bifunctional epoxide hydrolase 2 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor complex / hydrolase / OXIDOREDUCTASE-OXIDOREDUCTASE 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: 2.05 Å | ||||||
Authors | Amano, Y. / Yamaguchi, T. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y2p.cif.gz | 124.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y2p.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 4y2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/4y2p ftp://data.pdbj.org/pub/pdb/validation_reports/y2/4y2p | HTTPS FTP |
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-Related structure data
Related structure data | 4y2jC 4y2qC 4y2rC 4y2sC 4y2tC 4y2uC 4y2vC 4y2xC 4y2yC 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 / Fragment: UNP residues 1-555 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 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-3C5 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.37 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
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: 2.05→80.59 Å / Num. obs: 39866 / % possible obs: 98.8 % / Redundancy: 7.1 % / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→80.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.195 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.162 / 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: 30.944 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→80.59 Å
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Refine LS restraints |
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