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Yorodumi- PDB-1ya4: Crystal Structure of Human Liver Carboxylesterase 1 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ya4 | ||||||
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Title | Crystal Structure of Human Liver Carboxylesterase 1 in complex with tamoxifen | ||||||
Components | CES1 proteinCarboxylesterase 1 | ||||||
Keywords | HYDROLASE / Hydrolase Domain / Tamoxifen Complex | ||||||
Function / homology | Function and homology information cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / positive regulation of cholesterol metabolic process / Physiological factors / carboxylesterase ...cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / positive regulation of cholesterol metabolic process / Physiological factors / carboxylesterase / carboxylesterase activity / reverse cholesterol transport / cellular response to cholesterol / regulation of bile acid biosynthetic process / carboxylic ester hydrolase activity / Phase I - Functionalization of compounds / Aspirin ADME / cholesterol biosynthetic process / negative regulation of cholesterol storage / positive regulation of cholesterol efflux / cellular response to low-density lipoprotein particle stimulus / Metabolism of Angiotensinogen to Angiotensins / lipid catabolic process / cholesterol metabolic process / epithelial cell differentiation / lipid droplet / cholesterol homeostasis / response to toxic substance / endoplasmic reticulum lumen / endoplasmic reticulum / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Fleming, C.D. / Bencharit, S. / Edwards, C.C. / Hyatt, J.L. / Morton, C.L. / Howard-Williams, E.L. / Potter, P.M. / Redinbo, M.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ya4.cif.gz | 325.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ya4.ent.gz | 262.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ya4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/1ya4 ftp://data.pdbj.org/pub/pdb/validation_reports/ya/1ya4 | HTTPS FTP |
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-Related structure data
Related structure data | 1ya8C 1yahC 1yajC 1mx1S 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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 58672.227 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P23141, carboxylesterase |
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-Sugars , 2 types, 6 molecules
#2: Sugar | #3: Sugar | |
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-Non-polymers , 3 types, 203 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CTX / ( #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 3350, Sodium Chloride, Lithium Cloride, 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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.022 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 19, 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: 44285 / Num. obs: 34502 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 20 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6343 / Rsym value: 0.286 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MX1 Resolution: 3.2→48.53 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2015598.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.197 Å2 / ksol: 0.41025 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→48.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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