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Yorodumi- PDB-1zd4: Human soluble epoxide hydrolase 4-(3-cyclohexyluriedo)-hexanoic a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zd4 | ||||||
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Title | Human soluble epoxide hydrolase 4-(3-cyclohexyluriedo)-hexanoic 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 / Biosynthesis of maresins / soluble epoxide hydrolase / phospholipid dephosphorylation / epoxide metabolic process / lipid phosphatase activity / 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 / Biosynthesis of maresins / soluble epoxide hydrolase / phospholipid dephosphorylation / epoxide metabolic process / lipid phosphatase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 1zd4.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zd4.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zd4_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 1zd4_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | 1zd4_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 1zd4_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/1zd4 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/1zd4 | HTTPS FTP |
-Related structure data
Related structure data | 1zd2C 1zd3C 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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Components on special symmetry positions |
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Details | The second part of the biological assembly is generated by the symmetry_op=(-Y,-X,-Z+1/6) dx= 1 dy= 1 dz= 1 distance= 0.001 |
-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-NC6 / |
#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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 10, 2005 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→19.16 Å / Num. obs: 17736 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 8.59 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.33 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 6.8 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1S8O Resolution: 2.7→19.16 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→19.16 Å
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Refine LS restraints |
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