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- PDB-6qad: Human Butyrylcholinesterase in complex with ((S)-2-(butylamino)-N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qad | |||||||||
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Title | Human Butyrylcholinesterase in complex with ((S)-2-(butylamino)-N-(2-(4-(dimethylamino)cyclohexyl)ethyl)-3-(1H-indol-3-yl)propanamide | |||||||||
![]() | 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 / acetylcholinesterase activity / choline metabolic process / hydrolase activity, acting on ester bonds / nuclear envelope lumen / Aspirin ADME / 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 | ![]() | 131.2 KB | Display | ![]() |
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PDB format | ![]() | 98.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qaaC ![]() 6qabC ![]() 6qacC ![]() 6qaeC ![]() 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: Residues 1-28 are signal peptideNAG and FUC are N-glycosylationDMS is DMSOGOL is GlycerolMES is MES buffer333 is ligand 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 , 6 types, 76 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HUZ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HUZ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-DMS / | ||||||||
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#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-MES / | #8: Chemical | ChemComp-HUZ / ( | #9: Chemical | ChemComp-SO4 / #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.85 % |
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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: Sep 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.497→99.641 Å / Num. obs: 25229 / % possible obs: 90.69 % / Redundancy: 7.9 % / Biso Wilson estimate: 49.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09376 / Rpim(I) all: 0.03447 / Rrim(I) all: 0.1002 / Net I/σ(I): 15.41 |
Reflection shell | Resolution: 2.497→2.586 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.7896 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 2718 / CC1/2: 0.813 / Rpim(I) all: 0.2974 / Rrim(I) all: 0.8462 / % possible all: 99.89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P0I Resolution: 2.497→99.641 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / 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: 2.497→99.641 Å
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Refine LS restraints |
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LS refinement shell |
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