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- PDB-5am5: ligand complex structure of soluble epoxide hydrolase -

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Basic information

Entry
Database: PDB / ID: 5am5
Titleligand complex structure of soluble epoxide hydrolase
ComponentsBIFUNCTIONAL EPOXIDE HYDROLASE 2
KeywordsHYDROLASE
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
5-cyclohexyl-3-propyl-1H-pyridin-2-one / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsOster, L. / Tapani, S. / Xue, Y. / Kack, H.
CitationJournal: Drug Discov Today / Year: 2015
Title: Successful Generation of Structural Information for Fragment-Based Drug Discovery.
Authors: Oster, L. / Tapani, S. / Xue, Y. / Kack, H.
History
DepositionMar 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Feb 24, 2021Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_site
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.oligomeric_count ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6766
Polymers62,0031
Non-polymers6735
Water8,827490
1
A: BIFUNCTIONAL EPOXIDE HYDROLASE 2
hetero molecules

A: BIFUNCTIONAL EPOXIDE HYDROLASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,35212
Polymers124,0052
Non-polymers1,34610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area6050 Å2
ΔGint9 kcal/mol
Surface area42260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.324, 92.324, 244.472
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 / EPOXIDE HYDRATASE / SOLUBLE EPOXIDE HYDROLASE / SEH


Mass: 62002.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-6NZ / 5-cyclohexyl-3-propyl-1H-pyridin-2-one


Mass: 219.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.43 Å3/Da / Density % sol: 49.29 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.5418
DetectorType: RIGAKU A200-CU / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→244.47 Å / Num. obs: 29286 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 33.86 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 11.2
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 12 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 2.7 / % possible all: 97.6

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AHX
Resolution: 2.26→79.95 Å / Cor.coef. Fo:Fc: 0.9455 / Cor.coef. Fo:Fc free: 0.9048 / SU R Cruickshank DPI: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.336 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.21
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1485 5.08 %RANDOM
Rwork0.1679 ---
obs0.171 29251 98.12 %-
Displacement parametersBiso mean: 31.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.4241 Å20 Å20 Å2
2---1.4241 Å20 Å2
3---2.8483 Å2
Refinement stepCycle: LAST / Resolution: 2.26→79.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4323 0 44 490 4857
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014473HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.166057HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1552SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes643HARMONIC5
X-RAY DIFFRACTIONt_it4473HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion18.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion562SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5395SEMIHARMONIC4
LS refinement shellResolution: 2.26→2.34 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2741 146 5.41 %
Rwork0.1986 2551 -
all0.2028 2697 -
obs--98.12 %

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