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Yorodumi- PDB-1zd2: Human soluble epoxide hydrolase 4-(3-cyclohexyluriedo)-ethanoic a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zd2 | ||||||
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Title | Human soluble epoxide hydrolase 4-(3-cyclohexyluriedo)-ethanoic acid complex | ||||||
Components | epoxide hydrolase 2, cytoplasmic | ||||||
Keywords | HYDROLASE / 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 / Biosynthesis of maresins / soluble epoxide hydrolase / epoxide metabolic process / 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 / Biosynthesis of maresins / soluble epoxide hydrolase / epoxide metabolic process / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / dephosphorylation / phosphatase activity / peroxisomal matrix / toxic substance binding / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Gomez, G.A. / Morisseau, C. / Hammock, B.D. / Christianson, D.W. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zd2.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zd2.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zd2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zd2_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
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Full document | 1zd2_full_validation.pdf.gz | 466.7 KB | Display | |
Data in XML | 1zd2_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 1zd2_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/1zd2 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/1zd2 | HTTPS FTP |
-Related structure data
Related structure data | 1zd3C 1zd4C 1zd5C 1s8oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The 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= 2.007 |
-Components
#1: Protein | 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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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-NC3 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2004 Details: Single crystal, cylindrically bent, asymmetrically cut Si(220) crystal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 12983 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 9.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1s8o Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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