[English] 日本語
Yorodumi
- PDB-3pdc: Crystal structure of hydrolase domain of human soluble epoxide hy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pdc
TitleCrystal structure of hydrolase domain of human soluble epoxide hydrolase complexed with a benzoxazole inhibitor
ComponentsEpoxide hydrolase 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / epoxide hydrolase / hydrolase / hypertension / beta barrel / alpha/beta hydrolase fold / epoxide hydrolase fold / Acts on epoxides (alkene oxides / oxiranes) and arene oxides. Plays a role in xenobiotic metabolism by degrading potentially toxic epoxides. Also determines steady-state levels of physiological mediators. Has low phosphatase activity / Binds Mg2+ / Acetylation of lysine / cytoplasm / peroxisome / HYDROLASE-HYDROLASE INHIBITOR complex
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
Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold, catalytic domain ...Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZYI / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsKurumbail, R.G. / Williams, J.M.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Discovery of potent inhibitors of soluble epoxide hydrolase by combinatorial library design and structure-based virtual screening.
Authors: Xing, L. / McDonald, J.J. / Kolodziej, S.A. / Kurumbail, R.G. / Williams, J.M. / Warren, C.J. / O'Neal, J.M. / Skepner, J.E. / Roberds, S.L.
History
DepositionOct 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 24, 2021Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.oper_expression ..._pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.oper_expression / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epoxide hydrolase 2
B: Epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1824
Polymers78,6242
Non-polymers5572
Water3,441191
1
A: Epoxide hydrolase 2
hetero molecules

B: Epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1824
Polymers78,6242
Non-polymers5572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Unit cell
Length a, b, c (Å)46.523, 79.902, 89.318
Angle α, β, γ (deg.)90.000, 90.223, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two copies of the biological unit(unit 1)

-
Components

#1: Protein Epoxide hydrolase 2 / / Cytosolic epoxide hydrolase / CEH / Epoxide hydratase / Soluble epoxide hydrolase / SEH


Mass: 39312.016 Da / Num. of mol.: 2 / Fragment: Hydrolase domain (UNP residues 226 to 548)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf21 / References: UniProt: P34913, soluble epoxide hydrolase
#2: Chemical ChemComp-ZYI / N-(5-chloro-1,3-benzoxazol-2-yl)-2-cyclopentylacetamide


Mass: 278.734 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15ClN2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4
Details: 26-30% PEG6K, 0.1M sodium cacodylate, 0.07M ammonium acetate, 0.1M magnesium acetate, pH 7.4, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 22, 2005 / Details: osmic mirrors
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 18410 / Num. obs: 18410 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Χ2: 0.969 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.692.20.38116230.75180.9
2.69-2.82.30.33519040.73691.9
2.8-2.932.40.29318960.80193
2.93-3.082.50.24419110.83494.5
3.08-3.272.50.18818910.90594.3
3.27-3.522.50.14719560.96395.4
3.52-3.8820.12613091.16763.3
3.88-4.432.80.09618211.05389.4
4.43-5.5730.08320351.0898.6
5.57-203.10.06120641.20498.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
X-PLORphasing
X-PLORrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1S80

1s80


Resolution: 2.6→20 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Isotropic B factor refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.333 897 -Random selection of 5% of reflections
Rwork0.279 ---
all0.288 18003 --
obs0.279 18003 90 %-
Displacement parametersBiso max: 81.16 Å2 / Biso mean: 23.9855 Å2 / Biso min: 2 Å2
Refine analyzeLuzzati coordinate error obs: 0.426 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 38 191 5425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_improper_angle_d22.8
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.6-2.720.4341040.372X-RAY DIFFRACTION212580.9
5.17-200.2911380.252X-RAY DIFFRACTION253598.6

+
About Yorodumi

-
News

-
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

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

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

Read more