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- PDB-7q1m: Crystal structure of human butyrylcholinesterase in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7q1m | ||||||
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Title | Crystal structure of human butyrylcholinesterase in complex with N-[(2S)-3-[(cyclohexylmethyl)amino]-2-hydroxypropyl]-2,2-diphenylacetamide | ||||||
![]() | Cholinesterase | ||||||
![]() | HYDROLASE / Butyrylcholinesterase / Inhibitor / Complex | ||||||
Function / homology | ![]() cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / response to folic acid / choline binding / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / response to folic acid / choline binding / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / choline metabolic process / hydrolase activity, acting on ester bonds / acetylcholinesterase activity / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brazzolotto, X. / Panek, D. / Pasieka, A. / Malawska, B. / Nachon, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of new, highly potent and selective inhibitors of BuChE - design, synthesis, in vitro and in vivo evaluation and crystallography studies. Authors: Panek, D. / Pasieka, A. / Latacz, G. / Zareba, P. / Szczech, M. / Godyn, J. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Walczak, M. / Smolik, M. / Salat, K. ...Authors: Panek, D. / Pasieka, A. / Latacz, G. / Zareba, P. / Szczech, M. / Godyn, J. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Walczak, M. / Smolik, M. / Salat, K. / Hofner, G. / Wanner, K. / Wieckowska, A. / Malawska, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.2 KB | Display | ![]() |
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PDB format | ![]() | 193.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7q1nC ![]() 7q1oC ![]() 7q1pC ![]() 1p0iS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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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 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.) ![]() ![]() ![]() |
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-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
#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 #5: Sugar | |
-Non-polymers , 5 types, 130 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/8IS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/8IS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #6: Chemical | ChemComp-8IS / | #7: Chemical | ChemComp-GOL / | #8: Chemical | ChemComp-CL / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.59 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.791→109.4 Å / Num. obs: 19514 / % possible obs: 99.37 % / Redundancy: 26.4 % / Biso Wilson estimate: 64.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1703 / Rpim(I) all: 0.03358 / Rrim(I) all: 0.1737 / Net I/σ(I): 19.52 |
Reflection shell | Resolution: 2.791→2.89 Å / Redundancy: 21.9 % / Rmerge(I) obs: 1.633 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 1825 / CC1/2: 0.717 / Rpim(I) all: 0.3408 / Rrim(I) all: 1.671 / % possible all: 94.39 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1p0i Resolution: 2.79→109.4 Å / SU ML: 0.3763 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.6238 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: 76.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→109.4 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.8732128894 Å / Origin y: 32.37196149 Å / Origin z: 38.586805736 Å
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Refinement TLS group | Selection details: chain A |