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- PDB-5a7f: Comparison of the structure and activity of glycosylated and agly... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a7f | ||||||
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Title | Comparison of the structure and activity of glycosylated and aglycosylated Human Carboxylesterase 1 | ||||||
![]() | LIVER CARBOXYLESTERASE 1 | ||||||
![]() | HYDROLASE / ESTERASE | ||||||
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 / methyl indole-3-acetate esterase activity / regulation of bile acid secretion / carboxylesterase / Physiological factors ...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 / methyl indole-3-acetate esterase activity / 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 / triacylglycerol lipase activity / Aspirin ADME / negative regulation of cholesterol storage / cholesterol biosynthetic process / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / lipid catabolic process / epithelial cell differentiation / xenobiotic metabolic process / cholesterol metabolic process / lipid droplet / cholesterol homeostasis / response to toxic substance / endoplasmic reticulum lumen / endoplasmic reticulum / extracellular space / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arena de Souza, V. / Scott, D.J. / Charlton, M. / Walsh, M.A. / Owen, R.J. | ||||||
![]() | ![]() Title: Comparison of the Structure and Activity of Glycosylated and Aglycosylated Human Carboxylesterase 1. Authors: Arena De Souza, V. / Scott, D.J. / Nettleship, J.E. / Rahman, N. / Charlton, M.H. / Walsh, M.A. / Owens, R.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.2 KB | Display | ![]() |
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PDB format | ![]() | 177.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.5 KB | Display | ![]() |
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Full document | ![]() | 454.2 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a7gC ![]() 5a7hC ![]() 2h7cS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 58672.227 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-553 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P23141-3, UniProt: P23141*PLUS, carboxylesterase, carboxylesterase, methylumbelliferyl-acetate deacetylase | ||||
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#2: Sugar | ChemComp-NAG / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | N-ACETYL-D-GLUCOSAMIN | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: CRYSTALS WERE GROWN AT 20C IN 0.1 M MES/IMIDAZOLE, PH 6.5 CONTAINING 0.03 M EACH OF DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 10 % (W/V) POLYETHYLENE ...Details: CRYSTALS WERE GROWN AT 20C IN 0.1 M MES/IMIDAZOLE, PH 6.5 CONTAINING 0.03 M EACH OF DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 10 % (W/V) POLYETHYLENE GLYCOL 4000, 20% (W/V) GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 46879 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.86→1.88 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 71.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2H7C Resolution: 1.86→35.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.486 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.377 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→35.78 Å
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Refine LS restraints |
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