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- PDB-2hrq: Crystal structure of Human Liver Carboxylesterase 1 (hCE1) in cov... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hrq | |||||||||
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Title | Crystal structure of Human Liver Carboxylesterase 1 (hCE1) in covalent complex with the nerve agent Soman (GD) | |||||||||
![]() | Liver carboxylesterase 1 | |||||||||
![]() | HYDROLASE / carboxylesterase / soman | |||||||||
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. / Redinbo, M.R. | |||||||||
![]() | ![]() Title: Crystal Structures of Human Carboxylesterase 1 in Covalent Complexes with the Chemical Warfare Agents Soman and Tabun. Authors: Fleming, C.D. / Edwards, C.C. / Kirby, S.D. / Maxwell, D.M. / Potter, P.M. / Cerasoli, D.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 | ![]() | 652.4 KB | Display | ![]() |
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PDB format | ![]() | 528.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.5 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 130.3 KB | Display | |
Data in CIF | ![]() | 176.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hrrC ![]() 1mx1S 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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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 58672.227 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UK77, UniProt: P23141*PLUS, carboxylesterase |
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-Sugars , 3 types, 18 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/SIA.gif)
![](data/chem/img/SIA.gif)
#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose #4: Sugar | ChemComp-NAG / #5: Sugar | ChemComp-SIA / |
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-Non-polymers , 3 types, 1133 molecules ![](data/chem/img/GD7.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GD7 / ( #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Citrate pH 5.5, 8-11% PEG 3350, 0.1-0.4M Lithium Sulfate, 0.1M Lithium Chloride, 0.1M Sodium Chloride, 5% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 109797 / Num. obs: 109291 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.6 Å2 / Rsym value: 0.102 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 7.8 / Rsym value: 0.216 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry: 1MX1 Resolution: 2.7→42.91 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 86030.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.0313 Å2 / ksol: 0.360129 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→42.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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