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- PDB-3wke: Crystal structure of soluble epoxide hydrolase in complex with t-AUCB -

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Basic information

Entry
Database: PDB / ID: 3wke
TitleCrystal structure of soluble epoxide hydrolase in complex with t-AUCB
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase / 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 / Biosynthesis of maresins / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / 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 / Biosynthesis of maresins / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / dephosphorylation / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / cholesterol homeostasis / Peroxisomal protein import / regulation of cell growth / 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 / HAD superfamily/HAD-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / 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 / HAD superfamily/HAD-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / 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-AUB / PHOSPHATE ION / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsAmano, Y. / Yamaguchi, T. / Tanabe, E.
CitationJournal: Bioorg.Med.Chem. / Year: 2014
Title: Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography.
Authors: Amano, Y. / Yamaguchi, T. / Tanabe, E.
History
DepositionOct 18, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0464
Polymers63,5151
Non-polymers5323
Water1,45981
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0938
Polymers127,0292
Non-polymers1,0646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area5060 Å2
ΔGint-49 kcal/mol
Surface area42280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.948, 91.948, 243.942
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-748-

HOH

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Components

#1: Protein Bifunctional epoxide hydrolase 2 / Cytosolic epoxide hydrolase 2 / CEH / Epoxide hydratase / Soluble epoxide hydrolase / SEH / Lipid- ...Cytosolic epoxide hydrolase 2 / CEH / Epoxide hydratase / Soluble epoxide hydrolase / SEH / Lipid-phosphate phosphatase


Mass: 63514.512 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, lipid-phosphate phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-AUB / 4-[(trans-4-{[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbamoyl]amino}cyclohexyl)oxy]benzoic acid


Mass: 412.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Potassium phosphate, 0.2M Ammonium dihydrogen phosphate, 25%w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→40.02 Å / Num. obs: 15785 / % possible obs: 99.72 %
Reflection shellResolution: 2.75→2.822 Å / % possible all: 99.92

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→40.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.751 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25379 845 5.1 %RANDOM
Rwork0.17438 ---
obs0.17838 15785 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.464 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.75→40.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4323 0 36 81 4440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194466
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.986056
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78724.167192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.2415783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0381526
X-RAY DIFFRACTIONr_chiral_restr0.1050.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213359
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 70 -
Rwork0.235 1107 -
obs--99.92 %

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