+Open data
-Basic information
Entry | Database: PDB / ID: 5fp0 | ||||||
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Title | ligand complex structure of soluble epoxide hydrolase | ||||||
Components | BIFUNCTIONAL EPOXIDE HYDROLASE 2 | ||||||
Keywords | HYDROLASE | ||||||
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: 2.35 Å | ||||||
Authors | Xue, Y. / Olsson, T. / Johansson, C.A. / Oster, L. / Beisel, H.G. / Rohman, M. / Karis, D. / Backstrom, S. | ||||||
Citation | Journal: Chemmedchem / Year: 2016 Title: Fragment Screening of Soluble Epoxide Hydrolase for Lead Generation-Structure-Based Hit Evaluation and Chemistry Exploration. Authors: Xue, Y. / Olsson, T. / Johansson, C.A. / Oster, L. / Beisel, H. / Rohman, M. / Karis, D. / Backstrom, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fp0.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fp0.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fp0 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fp0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 62002.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase |
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#2: Chemical | ChemComp-DMS / |
#3: Chemical | ChemComp-SZC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 |
Detector | Type: PILATUS / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→67.04 Å / Num. obs: 24533 / % possible obs: 91.8 % / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Biso Wilson estimate: 42.58 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 17.9 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 4.6 / % possible all: 57.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→67.04 Å / Cor.coef. Fo:Fc: 0.9302 / Cor.coef. Fo:Fc free: 0.9026 / SU R Cruickshank DPI: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.541 / SU Rfree Blow DPI: 0.256 / SU Rfree Cruickshank DPI: 0.244 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 37.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→67.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.45 Å / Total num. of bins used: 12
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