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Yorodumi- PDB-2dqy: Crystal structure of human carboxylesterase in complex with chola... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dqy | ||||||
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Title | Crystal structure of human carboxylesterase in complex with cholate and palmitate | ||||||
Components | Liver carboxylesterase 1Carboxylesterase 1 | ||||||
Keywords | HYDROLASE / cholesterol metabolism / foam cells / macrophage / monocyte / atherosclerosis | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Bencharit, S. / Edwards, C.C. / Morton, C.L. / Howard-Williams, E.L. / Potter, P.M. / Redinbo, M.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Multisite promiscuity in the processing of endogenous substrates by human carboxylesterase 1 Authors: Bencharit, S. / Edwards, C.C. / Morton, C.L. / Howard-Williams, E.L. / Kuhn, P. / 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 | 2dqy.cif.gz | 331.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dqy.ent.gz | 263.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/2dqy ftp://data.pdbj.org/pub/pdb/validation_reports/dq/2dqy | HTTPS FTP |
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-Related structure data
Related structure data | 2dqzC 2dr0C 2h7cC 1mx1S C: citing same article (ref.) S: Starting model for refinement |
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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: 59787.527 Da / Num. of mol.: 3 / Fragment: residues 19-561 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23141, carboxylesterase |
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-Sugars , 2 types, 6 molecules
#2: Sugar | #3: Sugar | |
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-Non-polymers , 4 types, 313 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | #7: 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: 2.79 Å3/Da / Density % sol: 55.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 8% PEG 3350, 0.4M Li2SO4, 0.1M NaCl, 0.1M LiCl, 0.1M citrate (pH 5.5), 5% glycerol , pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SEALED TUBE / Type: RIGAKU / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 14, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 38284 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13 % / Rsym value: 0.11 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3→3.2 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.341 / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MX1 Resolution: 3→19.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2305620.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.7871 Å2 / ksol: 0.385922 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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