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Yorodumi- PDB-6hgx: Soluble epoxide hydrolase in complex with 1-(4-((4-(tert-butyl)mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hgx | ||||||
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Title | Soluble epoxide hydrolase in complex with 1-(4-((4-(tert-butyl)morpholin-2-yl)methoxy)phenyl)-3-cyclohexylurea | ||||||
Components | Bifunctional epoxide hydrolase 2 | ||||||
Keywords | HYDROLASE / Inhibitor / Complex / sEH | ||||||
Function / homology | Function and homology information lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / phospholipid dephosphorylation / 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 / soluble epoxide hydrolase / phospholipid dephosphorylation / 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 / 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 / molecular replacement / Resolution: 2.16 Å | ||||||
Authors | Kramer, J.S. / Pogoryelov, D. / Hiesinger, K. / Proschak, E. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2019 Title: Computer-Aided Selective Optimization of Side Activities of Talinolol. Authors: Hiesinger, K. / Kramer, J.S. / Achenbach, J. / Moser, D. / Weber, J. / Wittmann, S.K. / Morisseau, C. / Angioni, C. / Geisslinger, G. / Kahnt, A.S. / Kaiser, A. / Proschak, A. / Steinhilber, ...Authors: Hiesinger, K. / Kramer, J.S. / Achenbach, J. / Moser, D. / Weber, J. / Wittmann, S.K. / Morisseau, C. / Angioni, C. / Geisslinger, G. / Kahnt, A.S. / Kaiser, A. / Proschak, A. / Steinhilber, D. / Pogoryelov, D. / Wagner, K. / Hammock, B.D. / Proschak, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hgx.cif.gz | 151 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hgx.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/6hgx ftp://data.pdbj.org/pub/pdb/validation_reports/hg/6hgx | HTTPS FTP |
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-Related structure data
Related structure data | 6hgvC 6fr2S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 39648.531 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 BL21(DE3) (bacteria) References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-G3T / |
#4: 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: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1 uL protein solution Protein (5-10 mg/mL , 50 mM NaCl, 50 mM sodium phosphate, 10% glycerol (98%), 2 mM DTT at pH 7.4) was mixed in different ratios (2/1, 1/1, 1/2) with precipitant ...Details: 1 uL protein solution Protein (5-10 mg/mL , 50 mM NaCl, 50 mM sodium phosphate, 10% glycerol (98%), 2 mM DTT at pH 7.4) was mixed in different ratios (2/1, 1/1, 1/2) with precipitant solution (23 %-28 % (w/v) polyethylenglycol (PEG) 6000, 70 mM ammonium acetat, 200 mM magnesium acetat, 100 mM sodium cacodylate at pH 6.1-6.5) PH range: 6.0-6.55 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→52.85 Å / Num. obs: 21319 / % possible obs: 99.3 % / Redundancy: 6.362 % / Biso Wilson estimate: 40.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.143 / Χ2: 0.971 / Net I/σ(I): 10.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FR2 Resolution: 2.16→52.85 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 157.35 Å2 / Biso mean: 55.4339 Å2 / Biso min: 25.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.16→52.85 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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