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- PDB-1mx9: Crystal Structure of Human Liver Carboxylesterase in complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mx9 | ||||||
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Title | Crystal Structure of Human Liver Carboxylesterase in complexed with naloxone methiodide, a heroin analogue | ||||||
![]() | liver Carboxylesterase I | ||||||
![]() | HYDROLASE / esterase / heroin | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Bencharit, S. / Morton, C.L. / Xue, Y. / Potter, P.M. / Redinbo, M.R. | ||||||
![]() | ![]() Title: Structural Basis of Heroin and Cocaine Metabolism by a Promiscuous Human Drug-Processing Enzyme Authors: Bencharit, S. / Morton, C.L. / Xue, Y. / Potter, P.M. / Redinbo, M.R. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 12 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 12 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The authors have confirmed that human carboxylesterase 1 will form a trimer or hexamer in solution by Atomic Force Microscopy (AFM). They found the ratio of monomer:trimer:hexmer is ~ 10:44:46. 1MX1 contains a hexamer, 1MX5 contains 2 trimers. This entry contains two hexamers. The authors found that the trimer:hexmer ratio is dependent on the type and amount of ligands. | ||||||
Remark 999 | SEQUENCE THE AUTHOR'S SEQUENCE HAS NO GLN 362 (CALLED hCEv in: Kroetz DL, McBride OW, Gonzalez FJ. ...SEQUENCE THE AUTHOR'S SEQUENCE HAS NO GLN 362 (CALLED hCEv in: Kroetz DL, McBride OW, Gonzalez FJ.Glycosylation-dependent activity of baculovirus-expressed human liver carboxylesterases: cDNA cloning and characterization of two highly similar enzyme forms. Biochemistry 1993 Nov 2;32(43):11606-17) |
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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 | ![]() | 1012.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 162 KB | Display | |
Data in CIF | ![]() | 231.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Details | The biological assembly is two hexamers formed by four trimers in one asymmetric unit. |
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Components
#1: Protein | Mass: 60511.328 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-NLX / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG3350, Glycerol, lithium sulfate, lithium chloride, sodium chloride, sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 158131 / Num. obs: 157959 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 36.5 Å2 |
Reflection shell | Resolution: 2.9→3 Å / % possible all: 95.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Redundancy: 1.8 % / Num. measured all: 285255 / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3.08 Å / % possible obs: 95.7 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 2.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.7312 Å2 / ksol: 0.31259 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44 Å2
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Refine analyze | Luzzati coordinate error free: 0.49 Å / Luzzati sigma a free: 0.55 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→29.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 30 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.9 Å / Rfactor Rfree: 0.418 / Rfactor Rwork: 0.339 |