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- PDB-1zd3: Human soluble epoxide hydrolase 4-(3-cyclohexyluriedo)-butyric ac... -

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Basic information

Entry
Database: PDB / ID: 1zd3
TitleHuman soluble epoxide hydrolase 4-(3-cyclohexyluriedo)-butyric acid complex
Componentsepoxide hydrolase 2, cytoplasmic
KeywordsHYDROLASE / DOMAIN-SWAPPED DIMER
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 / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / HAD superfamily/HAD-like / 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 / haloacid dehalogenase-like hydrolase / 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
4-{[(CYCLOHEXYLAMINO)CARBONYL]AMINO}BUTANOIC ACID / PHOSPHATE ION / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGomez, G.A. / Morisseau, C. / Hammock, B.D. / Christianson, D.W.
CitationJournal: Protein Sci. / Year: 2006
Title: Human soluble epoxide hydrolase: structural basis of inhibition by 4-(3-cyclohexylureido)-carboxylic acids
Authors: Gomez, G.A. / Morisseau, C. / Hammock, B.D. / Christianson, D.W.
History
DepositionApr 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN 15P IS PART OF A PEG MOLECULE THAT INITIALLY WAS MODELED AS 15P, HOWVER THE MOLECULE ...HETEROGEN 15P IS PART OF A PEG MOLECULE THAT INITIALLY WAS MODELED AS 15P, HOWVER THE MOLECULE THOUGH IS AT A SPECIAL POSITION AND ONLY HALF WAS MODELED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: epoxide hydrolase 2, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5635
Polymers62,6861
Non-polymers1,8774
Water2,378132
1
A: epoxide hydrolase 2, cytoplasmic
hetero molecules

A: epoxide hydrolase 2, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,12610
Polymers125,3712
Non-polymers3,7558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Unit cell
Length a, b, c (Å)92.410, 92.410, 243.316
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe second part of the biological assembly is generated by the symmetry_op=(-X+Y,Y,-Z+1/2) dx=-1 dy= 0 dz= 0 distance= 0.334

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Components

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Protein , 1 types, 1 molecules A

#1: Protein epoxide hydrolase 2, cytoplasmic /


Mass: 62685.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Plasmid: ACHSEH1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34913, epoxide hydrolase

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Non-polymers , 5 types, 136 molecules

#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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#5: Chemical ChemComp-NC4 / 4-{[(CYCLOHEXYLAMINO)CARBONYL]AMINO}BUTANOIC ACID / 4-(3-CYCLOHEXYLURIEDO)-BUTYRIC ACID


Mass: 228.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N2O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: peg 3350, Tris, n-hexadecyl-B-d-maltoside, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2004
Details: Single crystal, cylindrically bent, asymmetrically cut Si(220) crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24352 / % possible obs: 86.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rsym value: 0.068 / Net I/σ(I): 23.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3 / Rsym value: 0.37 / % possible all: 50.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1S8O

1s8o


Resolution: 2.3→50 Å / Cross valid method: thhroughout / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 1365 -random
Rwork0.2117 ---
all-28239 --
obs-23477 83.1 %-
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 31 132 4495
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.9

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