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Open data
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Basic information
Entry | Database: PDB / ID: 5ake | ||||||
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Title | ligand complex structure of soluble epoxide hydrolase | ||||||
![]() | BIFUNCTIONAL EPOXIDE HYDROLASE 2 | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Oster, L. / Tapani, S. / Xue, Y. / Kack, H. | ||||||
![]() | ![]() Title: Successful Generation of Structural Information for Fragment-Based Drug Discovery. Authors: Oster, L. / Tapani, S. / Xue, Y. / Kack, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.4 KB | Display | ![]() |
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PDB format | ![]() | 101.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ahxSC ![]() 5ai0C ![]() 5ai4C ![]() 5ai5C ![]() 5ai6C ![]() 5ai8C ![]() 5ai9C ![]() 5aiaC ![]() 5aibC ![]() 5aicC ![]() 5ak3C ![]() 5ak4C ![]() 5ak5C ![]() 5ak6C ![]() 5akgC ![]() 5akhC ![]() 5akiC ![]() 5akjC ![]() 5akkC ![]() 5aklC ![]() 5akxC ![]() 5akyC ![]() 5akzC ![]() 5aldC ![]() 5aleC ![]() 5alfC ![]() 5algC ![]() 5alhC ![]() 5aliC ![]() 5aljC ![]() 5alkC ![]() 5allC ![]() 5almC ![]() 5alnC ![]() 5aloC ![]() 5alpC ![]() 5alqC ![]() 5alrC ![]() 5alsC ![]() 5altC ![]() 5aluC ![]() 5alvC ![]() 5alwC ![]() 5alxC ![]() 5alyC ![]() 5alzC ![]() 5am0C ![]() 5am1C ![]() 5am2C ![]() 5am3C ![]() 5am4C ![]() 5am5C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 62002.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase |
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-Non-polymers , 5 types, 359 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/6N0.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/6N0.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-6N0 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.54 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU A200-CU / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→243.93 Å / Num. obs: 29943 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 37.01 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.26→2.38 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 5.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5AHX Resolution: 2.26→80.24 Å / Cor.coef. Fo:Fc: 0.9386 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.331 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.213 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 35.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→80.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.34 Å / Total num. of bins used: 15
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