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- PDB-6qae: Human Butyrylcholinesterase in complex with (S)-N2-butyl-N1-(2-cy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qae | |||||||||
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Title | Human Butyrylcholinesterase in complex with (S)-N2-butyl-N1-(2-cycloheptylethyl)-3-(1H-indol-3-yl)-N1,N2-dimethylpropane-1,2-diamine | |||||||||
![]() | 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. / Nachon, F. / Harst, M. / Knez, D. / Gobec, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Tryptophan-derived butyrylcholinesterase inhibitors as promising leads against Alzheimer's disease. Authors: Meden, A. / Knez, D. / Jukic, M. / Brazzolotto, X. / Grsic, M. / Pislar, A. / Zahirovic, A. / Kos, J. / Nachon, F. / Svete, J. / Gobec, S. / Groselj, U. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.1 KB | Display | ![]() |
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PDB format | ![]() | 98.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qaaC ![]() 6qabC ![]() 6qacC ![]() 6qadC ![]() 1p0iS S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63029.668 Da / Num. of mol.: 1 / Mutation: N45Q, N483Q, N509Q, N514Q, 558STOP Source method: isolated from a genetically manipulated source Details: NAG and FUC are Glycosylation / 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 | #4: Sugar | |
-Non-polymers , 3 types, 116 molecules ![](data/chem/img/HUK.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-HUK / | ||
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#6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.487→54.812 Å / Num. obs: 26948 / % possible obs: 99.86 % / Redundancy: 8.3 % / Biso Wilson estimate: 54.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07352 / Rpim(I) all: 0.02699 / Rrim(I) all: 0.07849 / Net I/σ(I): 19.09 |
Reflection shell | Resolution: 2.487→2.576 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.8433 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 2645 / CC1/2: 0.823 / Rpim(I) all: 0.3042 / Rrim(I) all: 0.8978 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P0I Resolution: 2.487→54.812 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.487→54.812 Å
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Refine LS restraints |
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LS refinement shell |
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