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- PDB-6hgx: Soluble epoxide hydrolase in complex with 1-(4-((4-(tert-butyl)mo... -

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Basic information

Entry
Database: PDB / ID: 6hgx
TitleSoluble epoxide hydrolase in complex with 1-(4-((4-(tert-butyl)morpholin-2-yl)methoxy)phenyl)-3-cyclohexylurea
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / Inhibitor / Complex / sEH
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-G3T / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å
AuthorsKramer, J.S. / Pogoryelov, D. / Hiesinger, K. / Proschak, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Else-Kroener-Fresenius Stiftung TRIP Graduate School Germany
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Computer-Aided Selective Optimization of Side Activities of Talinolol.
Authors: Hiesinger, K. / Kramer, J.S. / Achenbach, J. / Moser, D. / Weber, J. / Wittmann, S.K. / Morisseau, C. / Angioni, C. / Geisslinger, G. / Kahnt, A.S. / Kaiser, A. / Proschak, A. / Steinhilber, ...Authors: Hiesinger, K. / Kramer, J.S. / Achenbach, J. / Moser, D. / Weber, J. / Wittmann, S.K. / Morisseau, C. / Angioni, C. / Geisslinger, G. / Kahnt, A.S. / Kaiser, A. / Proschak, A. / Steinhilber, D. / Pogoryelov, D. / Wagner, K. / Hammock, B.D. / Proschak, E.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Jan 17, 2024Group: 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

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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)40,0623
Polymers39,6491
Non-polymers4142
Water2,018112
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1256
Polymers79,2972
Non-polymers8284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)79.800, 92.000, 105.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-744-

HOH

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 39648.531 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 BL21(DE3) (bacteria)
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-G3T / 1-[4-[[(2~{S})-4-~{tert}-butylmorpholin-2-yl]methoxy]phenyl]-3-cyclohexyl-urea


Mass: 389.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H35N3O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1 uL protein solution Protein (5-10 mg/mL , 50 mM NaCl, 50 mM sodium phosphate, 10% glycerol (98%), 2 mM DTT at pH 7.4) was mixed in different ratios (2/1, 1/1, 1/2) with precipitant ...Details: 1 uL protein solution Protein (5-10 mg/mL , 50 mM NaCl, 50 mM sodium phosphate, 10% glycerol (98%), 2 mM DTT at pH 7.4) was mixed in different ratios (2/1, 1/1, 1/2) with precipitant solution (23 %-28 % (w/v) polyethylenglycol (PEG) 6000, 70 mM ammonium acetat, 200 mM magnesium acetat, 100 mM sodium cacodylate at pH 6.1-6.5)
PH range: 6.0-6.55

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2017
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.15→52.85 Å / Num. obs: 21319 / % possible obs: 99.3 % / Redundancy: 6.362 % / Biso Wilson estimate: 40.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.143 / Χ2: 0.971 / Net I/σ(I): 10.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.216.4071.0161.3914360.7241.10491
2.21-2.276.7410.8341.8615080.7910.90599.9
2.27-2.336.6430.6672.3714880.8850.725100
2.33-2.416.5770.5822.7514380.9030.634100
2.41-2.496.4720.5193.114060.930.56699.9
2.49-2.576.2270.4263.7513600.9540.467100
2.57-2.675.7440.3224.7113050.970.35599.9
2.67-2.785.7560.2775.6512770.9780.30599.9
2.78-2.96.260.2167.5811880.9870.236100
2.9-3.046.1250.199.6511600.9870.20999.8
3.04-3.216.7120.18513.1511180.990.201100
3.21-3.46.7990.15715.5410470.990.1799.9
3.4-3.646.5250.12618.679930.9920.137100
3.64-3.935.8760.10519.979200.9940.11699.9
3.93-4.316.4660.08823.568480.9950.095100
4.31-4.816.7250.07326.167860.9970.08100
4.81-5.566.6010.07725.836920.9960.084100
5.56-6.816.2190.07324.115970.9960.08100
6.81-9.635.8320.0528.824700.9980.05599.8
9.63-52.855.950.04234.32820.9970.04798.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FR2

6fr2


Resolution: 2.16→52.85 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.22
RfactorNum. reflection% reflection
Rfree0.2536 2043 9.64 %
Rwork0.2023 --
obs0.2073 21197 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.35 Å2 / Biso mean: 55.4339 Å2 / Biso min: 25.59 Å2
Refinement stepCycle: final / Resolution: 2.16→52.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 29 112 2689
Biso mean--95.05 53.13 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082683
X-RAY DIFFRACTIONf_angle_d1.0063647
X-RAY DIFFRACTIONf_chiral_restr0.054378
X-RAY DIFFRACTIONf_plane_restr0.006470
X-RAY DIFFRACTIONf_dihedral_angle_d24.1311002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.21030.32011330.299712431376100
2.2103-2.26560.34861340.279312421376100
2.2656-2.32680.3021330.25881254138799
2.3268-2.39530.32511350.268212731408100
2.3953-2.47260.34751340.27412581392100
2.4726-2.5610.29691340.276912591393100
2.561-2.66350.34951370.287212691406100
2.6635-2.78470.36371360.292412841420100
2.7847-2.93150.27961340.255212501384100
2.9315-3.11520.34611370.245712811418100
3.1152-3.35560.24021360.195912801416100
3.3556-3.69330.23511370.17312881425100
3.6933-4.22750.18141370.150312921429100
4.2275-5.32540.20141400.140913091449100
5.3254-52.86580.21971460.183513721518100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1191.0245-0.15353.55380.0272.7071-0.0629-0.0614-0.1676-0.1444-0.0068-0.16230.09730.10450.0330.19720.00380.0410.22810.01350.28-4.0704-13.7721-32.844
23.2975-3.13670.67413.22340.10094.4811-0.4563-0.3036-1.4579-0.17930.50750.64771.2944-0.7960.04480.8525-0.13270.1040.56140.05450.7426-13.3155-31.2642-44.8033
34.18453.0785-3.9974.3593-1.68034.5688-0.3691-0.2598-0.6804-0.32810.2148-0.15370.86550.32220.20540.4434-0.0246-0.08790.46470.06010.5156-24.6448-20.8989-43.3282
42.9719-0.15120.01382.9229-0.1672.2203-0.0899-0.0144-0.2692-0.17510.08510.07340.2147-0.1057-0.02140.3187-0.05350.0280.25270.02760.3145-14.1692-20.6689-32.1476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 229 through 370 )A229 - 370
2X-RAY DIFFRACTION2chain 'A' and (resid 371 through 399 )A371 - 399
3X-RAY DIFFRACTION3chain 'A' and (resid 400 through 421 )A400 - 421
4X-RAY DIFFRACTION4chain 'A' and (resid 422 through 547 )A422 - 547

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