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Yorodumi- PDB-7amz: Crystal structure of human Butyrylcholinesterase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7amz | ||||||
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Title | Crystal structure of human Butyrylcholinesterase in complex with N-((2S,3R)-4-((2,2-dimethylpropyl)amino)-3-hydroxy-1-phenylbutan-2-yl)-2,2-diphenylacetamide | ||||||
Components | Cholinesterase | ||||||
Keywords | HYDROLASE / Butyrylcholinesterase / Inhibitor / Complex | ||||||
Function / homology | Function and homology information cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / acetylcholinesterase activity / choline metabolic process / hydrolase activity, acting on ester bonds / Aspirin ADME / nuclear envelope lumen / Synthesis of PC / Synthesis, secretion, and deacylation of Ghrelin / catalytic activity / response to glucocorticoid / xenobiotic metabolic process / learning / amyloid-beta binding / blood microparticle / negative regulation of cell population proliferation / endoplasmic reticulum lumen / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Brazzolotto, X. / Pasieka, A. / Panek, D. / Wieckowska, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2021 Title: Discovery of multifunctional anti-Alzheimer's agents with a unique mechanism of action including inhibition of the enzyme butyrylcholinesterase and gamma-aminobutyric acid transporters. Authors: Pasieka, A. / Panek, D. / Jonczyk, J. / Godyn, J. / Szalaj, N. / Latacz, G. / Tabor, J. / Mezeiova, E. / Chantegreil, F. / Dias, J. / Knez, D. / Lu, J. / Pi, R. / Korabecny, J. / ...Authors: Pasieka, A. / Panek, D. / Jonczyk, J. / Godyn, J. / Szalaj, N. / Latacz, G. / Tabor, J. / Mezeiova, E. / Chantegreil, F. / Dias, J. / Knez, D. / Lu, J. / Pi, R. / Korabecny, J. / Brazzolotto, X. / Gobec, S. / Hofner, G. / Wanner, K. / Wieckowska, A. / Malawska, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7amz.cif.gz | 158.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7amz.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 7amz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/7amz ftp://data.pdbj.org/pub/pdb/validation_reports/am/7amz | HTTPS FTP |
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-Related structure data
Related structure data | 1p0iS 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, 1 molecules A
#1: Protein | Mass: 59713.512 Da / Num. of mol.: 1 Mutation: N17Q, N455Q, N481Q, N486Q and 530STOP mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase |
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-Sugars , 4 types, 7 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #6: Sugar | ChemComp-SIA / | |
-Non-polymers , 5 types, 149 molecules
#5: Chemical | #7: Chemical | ChemComp-RNZ / | #8: Chemical | ChemComp-MES / | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.19 Å3/Da / Density % sol: 61.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98012 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98012 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→48.81 Å / Num. obs: 36839 / % possible obs: 99.94 % / Redundancy: 26.7 % / Biso Wilson estimate: 47.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1772 / Rpim(I) all: 0.03492 / Rrim(I) all: 0.1807 / Net I/σ(I): 16.76 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 26 % / Rmerge(I) obs: 2.804 / Mean I/σ(I) obs: 1.68 / Num. unique obs: 3619 / CC1/2: 0.666 / Rpim(I) all: 0.5596 / Rrim(I) all: 2.86 / % possible all: 99.81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1p0i Resolution: 2.25→48.81 Å / SU ML: 0.2791 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2828 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→48.81 Å
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Refine LS restraints |
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LS refinement shell |
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