|Entry||Database: PDB / ID: 3otq|
|Title||Soluble Epoxide Hydrolase in complex with pyrazole antagonist|
|Components||Epoxide hydrolase 2|
|Keywords||HYDROLASE / epoxide hydrolase|
|Function / homology|
Function and homology information
10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / lipid-phosphate phosphatase / phospholipid dephosphorylation / stilbene catabolic process / epoxide metabolic process / lipid phosphatase activity / Biosynthesis of maresins / soluble epoxide hydrolase / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) ...10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / lipid-phosphate phosphatase / phospholipid dephosphorylation / stilbene catabolic process / epoxide metabolic process / lipid phosphatase activity / 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 / hydrolase activity / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / alpha/beta hydrolase fold / HAD superfamily/HAD-like ...Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / alpha/beta hydrolase fold / HAD superfamily/HAD-like / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold, catalytic domain / DNA polymerase; domain 1 / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MZL / Bifunctional epoxide hydrolase 2
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å|
|Citation||Journal: Bioorg.Med.Chem.Lett. / Year: 2010|
Title: Substituted pyrazoles as novel sEH antagonist: investigation of key binding interactions within the catalytic domain.
Authors: Lo, H.Y. / Man, C.C. / Fleck, R.W. / Farrow, N.A. / Ingraham, R.H. / Kukulka, A. / Proudfoot, J.R. / Betageri, R. / Kirrane, T. / Patel, U. / Sharma, R. / Hoermann, M.A. / Kabcenell, A. / Lombaert, S.D.
|Structure viewer||Molecule: |
Downloads & links
A: Epoxide hydrolase 2
A: Epoxide hydrolase 2
A: Epoxide hydrolase 2
|#1: Protein|| |
Mass: 62685.617 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 (E. coli) / References: UniProt: P34913, soluble epoxide hydrolase
|#2: Chemical|| ChemComp-MZL / |
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION|
|Crystal||Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 %|
|Diffraction source||Source: ROTATING ANODE / Type: RIGAKU RUH3R|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Relative weight: 1|
|Reflection||Resolution: 3→50 Å / Num. obs: 12861|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å|
|Refinement step||Cycle: LAST / Resolution: 3→50 Å|
-Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
- Version 3 of the EMDB header file is now the official format.
- The previous official version 1.9 will be removed from the archive.
Related info.:EMDB header
External links:wwPDB to switch to version 3 of the EMDB data model
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
+Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi