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- PDB-7p4k: Soluble epoxide hydrolase in complex with FL217 -

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Basic information

Entry
Database: PDB / ID: 7p4k
TitleSoluble epoxide hydrolase in complex with FL217
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / Complex / Structural Genomics / Structural Genomics Consortium / SGC
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
Similarity search - Domain/homology
Chem-5IV / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsNi, X. / Kramer, J.S. / Lillich, F. / Proschak, E. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Based Design of Dual Partial Peroxisome Proliferator-Activated Receptor gamma Agonists/Soluble Epoxide Hydrolase Inhibitors.
Authors: Lillich, F.F. / Willems, S. / Ni, X. / Kilu, W. / Borkowsky, C. / Brodsky, M. / Kramer, J.S. / Brunst, S. / Hernandez-Olmos, V. / Heering, J. / Schierle, S. / Kestner, R.I. / Mayser, F.M. / ...Authors: Lillich, F.F. / Willems, S. / Ni, X. / Kilu, W. / Borkowsky, C. / Brodsky, M. / Kramer, J.S. / Brunst, S. / Hernandez-Olmos, V. / Heering, J. / Schierle, S. / Kestner, R.I. / Mayser, F.M. / Helmstadter, M. / Gobel, T. / Weizel, L. / Namgaladze, D. / Kaiser, A. / Steinhilber, D. / Pfeilschifter, W. / Kahnt, A.S. / Proschak, A. / Chaikuad, A. / Knapp, S. / Merk, D. / Proschak, E.
History
DepositionJul 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
B: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3884
Polymers79,2972
Non-polymers1,0912
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint3 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.820, 79.326, 88.599
Angle α, β, γ (deg.)90.000, 126.650, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 229 - 547 / Label seq-ID: 11 - 329

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 39648.531 Da / Num. of mol.: 2
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-5IV / ~{N}-[[4-(cyclopropylsulfonylamino)-2-(trifluoromethyl)phenyl]methyl]-1-[(3-fluorophenyl)methyl]indole-5-carboxamide


Mass: 545.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H23F4N3O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 28 % (w/v) polyethylenglycol (PEG) 6000, 70 mM ammonium acetat, 200 mM magnesium acetat, 100 mM sodium cacodylate at pH 6.13

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.15→44.02 Å / Num. obs: 35542 / % possible obs: 92 % / Redundancy: 2.5 % / CC1/2: 0.996 / Net I/σ(I): 7.4
Reflection shellResolution: 2.15→2.22 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3151 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FR2

6fr2


Resolution: 2.15→44.02 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.128 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2437 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 1811 5.1 %RANDOM
Rwork0.1772 ---
obs0.1796 33693 91.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.61 Å2 / Biso mean: 49.194 Å2 / Biso min: 27.83 Å2
Baniso -1Baniso -2Baniso -3
1-3.84 Å20 Å21.75 Å2
2---5.72 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 2.15→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4865 0 76 74 5015
Biso mean--57.58 41.92 -
Num. residues----616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135121
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174659
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.646970
X-RAY DIFFRACTIONr_angle_other_deg1.1921.58510738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4655619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90322.112251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64615816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6051528
X-RAY DIFFRACTIONr_chiral_restr0.0630.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026047
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021213
Refine LS restraints NCS

Ens-ID: 1 / Number: 10084 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 148 -
Rwork0.238 2527 -
all-2675 -
obs--93.6 %
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)
11.2408-0.2316-0.43632.26610.78011.67160.02580.0410.02810.03040.0018-0.1265-0.13810.0092-0.02760.0905-0.01030.00150.13130.00050.0539-6.1248-3.632539.8878
21.5054-0.031-0.252.19330.22452.2790.05660.1239-0.1904-0.1901-0.0142-0.22980.10140.1892-0.04240.0420.0310.01330.1195-0.04940.0645-1.2013-14.895331.4266
30.9625-0.0534-0.41191.74170.47441.6656-0.04910.0149-0.0120.2041-0.05710.027-0.1185-0.1910.10610.2050.0065-0.01280.1463-0.02060.0076-23.935311.850762.6433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A229 - 352
2X-RAY DIFFRACTION2A353 - 547
3X-RAY DIFFRACTION3B229 - 547

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