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Yorodumi- PDB-5mwa: human sEH Phosphatase in complex with 3-4-3,4-dichlorophenyl-5-ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mwa | ||||||
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Title | human sEH Phosphatase in complex with 3-4-3,4-dichlorophenyl-5-phenyl-1,3-oxazol-2-yl-benzoic-acid | ||||||
Components | Bifunctional epoxide hydrolase 2 | ||||||
Keywords | HYDROLASE / Phosphatase / Complex / Inhibitor / Magnesium / human soluble epoxide hydrolase / sEH | ||||||
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: 1.55 Å | ||||||
Authors | Kramer, J.S. / Pogoryelov, D. / Sorrell, F.J. / Fox, N. / Chaikuad, A. / Knapp, S. / Proschak, E. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: Discovery of first in vivo active inhibitors of soluble epoxide hydrolase (sEH) phosphatase domain. Authors: Kramer, J.S. / Woltersdorf, S. / Duflot, T. / Hiesinger, K. / Lillich, F.F. / Knoll, F. / Wittmann, S.K. / Klingler, F.M. / Brunst, S. / Chaikuad, A. / Morisseau, C. / Hammock, B.D. / ...Authors: Kramer, J.S. / Woltersdorf, S. / Duflot, T. / Hiesinger, K. / Lillich, F.F. / Knoll, F. / Wittmann, S.K. / Klingler, F.M. / Brunst, S. / Chaikuad, A. / Morisseau, C. / Hammock, B.D. / Buccellati, C. / Sala, A. / Rovati, G.E. / Leuillier, M. / Fraineau, S. / Rondeaux, J. / Hernandez Olmos, V. / Heering, J. / Merk, D. / Pogoryelov, D. / Steinhilber, D. / Knapp, S. / Bellien, J. / Proschak, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mwa.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mwa.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 5mwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/5mwa ftp://data.pdbj.org/pub/pdb/validation_reports/mw/5mwa | HTTPS FTP |
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-Related structure data
Related structure data | 5aluS 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: 27400.857 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-8S9 / |
#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: 2.28 Å3/Da / Density % sol: 46.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein solution: 20 mM Tris, 100 mM NaCl, 0,5 mM TCEP, pH7.5 (HCl) with 30mg/mL protein and 2,08% of a 50 mM inhibitor DMSO stock Precipitant solution: 25% PEG3350 - 0,1M bis-tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Oxford Instruments Cryojet XL |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016 Details: Kirkpatrick Baez (KB) bimorph mirror pair for horizontal and vertical focussing |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→42.86 Å / Num. obs: 31021 / % possible obs: 89 % / Observed criterion σ(F): 1.55 / Redundancy: 6.4 % / Biso Wilson estimate: 14.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07485 / Net I/σ(I): 12.39 |
Reflection shell | Resolution: 1.55→1.605 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.56 / CC1/2: 0.709 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5alu Resolution: 1.55→42.86 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||
Displacement parameters | Biso mean: 18.49 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→42.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3391→42.86 Å
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