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- PDB-3i28: Crystal Structure of soluble epoxide Hydrolase -

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Basic information

Entry
Database: PDB / ID: 3i28
TitleCrystal Structure of soluble epoxide Hydrolase
ComponentsEpoxide hydrolase 2
KeywordsHYDROLASE / Aromatic hydrocarbons catabolism / Detoxification / Magnesium / Metal-binding / Peroxisome
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 / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / HAD superfamily/HAD-like / Alpha/beta hydrolase fold-1 / HAD superfamily ...Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / haloacid dehalogenase-like hydrolase / 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-34N / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFarrow, N.A.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Structure-based optimization of arylamides as inhibitors of soluble epoxide hydrolase.
Authors: Eldrup, A.B. / Soleymanzadeh, F. / Taylor, S.J. / Muegge, I. / Farrow, N.A. / Joseph, D. / McKellop, K. / Man, C.C. / Kukulka, A. / De Lombaert, S.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 24, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_site
Item: _pdbx_struct_assembly_prop.biol_id / _struct_site.pdbx_auth_asym_id ..._pdbx_struct_assembly_prop.biol_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1222
Polymers62,6861
Non-polymers4361
Water2,738152
1
A: Epoxide hydrolase 2
hetero molecules

A: Epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,2444
Polymers125,3712
Non-polymers8732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area4300 Å2
ΔGint-7 kcal/mol
Surface area42900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.410, 92.410, 243.983
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


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-34N / 4-cyano-N-{(3S)-3-(4-fluorophenyl)-3-[4-(methylsulfonyl)phenyl]propyl}benzamide


Mass: 436.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21FN2O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.72 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionHighest resolution: 1.95 Å / Num. obs: 45221 / Biso Wilson estimate: 34.33 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_6refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→36.252 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.815 / SU ML: 0.18 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 2271 5.02 %
Rwork0.214 --
obs0.216 45221 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.062 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 121.3 Å2 / Biso mean: 40.436 Å2 / Biso min: 19.87 Å2
Baniso -1Baniso -2Baniso -3
1-2.902 Å20 Å2-0 Å2
2--2.902 Å2-0 Å2
3----5.804 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 31 152 4499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084455
X-RAY DIFFRACTIONf_angle_d1.1316038
X-RAY DIFFRACTIONf_chiral_restr0.08658
X-RAY DIFFRACTIONf_plane_restr0.005776
X-RAY DIFFRACTIONf_dihedral_angle_d17.8311655
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.9920.2751230.2112625274899
1.992-2.0390.2531490.2142613276299
2.039-2.090.2711440.2122624276899
2.09-2.1460.2561660.2052618278499
2.146-2.2090.3031440.2082645278999
2.209-2.2810.2531250.2032654277999
2.281-2.3620.2681200.2092681280199
2.362-2.4570.2871320.2282669280199
2.457-2.5690.2891300.2322699282999
2.569-2.7040.3081300.23126972827100
2.704-2.8730.2541490.2372701285099
2.873-3.0950.291690.23526892858100
3.095-3.4060.2491530.22227192872100
3.406-3.8990.2491480.20527622910100
3.899-4.910.2081460.1752759290598
4.91-36.2590.241430.2252795293893

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