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- PDB-4y2x: Structure of soluble epoxide hydrolase in complex with 2-({[2-(ad... -

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Basic information

Entry
Database: PDB / ID: 4y2x
TitleStructure of soluble epoxide hydrolase in complex with 2-({[2-(adamantan-1-yl)ethyl]amino}methyl)phenol
ComponentsBifunctional epoxide hydrolase 2
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / hydrolase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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-4A0 / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAmano, Y. / Yamaguchi, T.
CitationJournal: Bioorg.Med.Chem. / Year: 2015
Title: Identification of N-ethylmethylamine as a novel scaffold for inhibitors of soluble epoxide hydrolase by crystallographic fragment screening
Authors: Amano, Y. / Tanabe, E. / Yamaguchi, T.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8243
Polymers63,5151
Non-polymers3102
Water1267
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6486
Polymers127,0292
Non-polymers6194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area4510 Å2
ΔGint-25 kcal/mol
Surface area42950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.731, 92.731, 243.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Bifunctional epoxide hydrolase 2


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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-4A0 / 2-[({2-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-yl]ethyl}amino)methyl]phenol


Mass: 285.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H27NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Potassium phosphate, Ammonium dihydrogen phosphate, PEG3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 21937 / % possible obs: 98.4 % / Redundancy: 6.9 % / Net I/σ(I): 2.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S8O
Resolution: 2.5→80.31 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.873 / SU B: 11.485 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.642 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27827 1121 5.1 %RANDOM
Rwork0.21963 ---
obs0.22254 20770 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.869 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.5→80.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4323 0 22 7 4352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9786041
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25524.167192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94615783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5971526
X-RAY DIFFRACTIONr_chiral_restr0.110.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213351
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_it2.1433.4672183
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3555.1932727
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8063.6542273
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.02328.8826610
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 93 -
Rwork0.298 1498 -
obs--99.94 %

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