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- PDB-1yaj: Crystal Structure of Human Liver Carboxylesterase in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yaj | ||||||
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Title | Crystal Structure of Human Liver Carboxylesterase in complex with benzil | ||||||
![]() | CES1 protein | ||||||
![]() | HYDROLASE / Carboxylesterase / Benzil / Inhibition | ||||||
Function / homology | ![]() cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / carboxylesterase / Physiological factors / carboxylesterase activity ...cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / carboxylesterase / Physiological factors / carboxylesterase activity / cellular response to cholesterol / regulation of bile acid biosynthetic process / positive regulation of cholesterol metabolic process / reverse cholesterol transport / carboxylic ester hydrolase activity / Phase I - Functionalization of compounds / Aspirin ADME / negative regulation of cholesterol storage / cholesterol biosynthetic process / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / Metabolism of Angiotensinogen to Angiotensins / lipid catabolic process / epithelial cell differentiation / cholesterol metabolic process / lipid droplet / cholesterol homeostasis / response to toxic substance / endoplasmic reticulum lumen / endoplasmic reticulum / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fleming, C.D. / Bencharit, S. / Edwards, C.C. / Hyatt, J.L. / Morton, C.M. / Howard-Williams, E.L. / Potter, P.M. / Redinbo, M.R. | ||||||
![]() | ![]() Title: Structural insights into drug processing by human carboxylesterase 1: tamoxifen, mevastatin, and inhibition by benzil. Authors: Fleming, C.D. / Bencharit, S. / Edwards, C.C. / Hyatt, J.L. / Tsurkan, L. / Bai, F. / Fraga, C. / Morton, C.L. / Howard-Williams, E.L. / Potter, P.M. / Redinbo, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 1012.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.5 MB | Display | ![]() |
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Full document | ![]() | 4.8 MB | Display | |
Data in XML | ![]() | 257.4 KB | Display | |
Data in CIF | ![]() | 338.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ya4C ![]() 1ya8C ![]() 1yahC ![]() 1mx5S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 58672.227 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 24 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/SIA.gif)
![](data/chem/img/SIA.gif)
#2: Sugar | ChemComp-NAG / #3: Sugar | ChemComp-SIA / |
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-Non-polymers , 3 types, 522 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-BEZ / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 3350, Sodium Chloride, Lithium Chloride, Lithium Sulfate, Citrate, Glycerol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.022 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 124749 / Num. obs: 124749 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.156 / Rsym value: 0.156 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.446 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MX5 Resolution: 3.2→54.56 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2488896.98 / Data cutoff high rms absF: 2488896.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.9222 Å2 / ksol: 0.372895 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→54.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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