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- PDB-5dyt: Crystal structure of human butyrylcholinesterase in complex with ... -
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Basic information
Entry | Database: PDB / ID: 5dyt | |||||||||
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Title | Crystal structure of human butyrylcholinesterase in complex with N-((1-benzylpiperidin-3-yl)methyl)-N-methylnaphthalene-2-sulfonamide | |||||||||
![]() | Cholinesterase | |||||||||
![]() | HYDROLASE / human butyrylcholinesterase / AD / alzheimer disease / sulfonamide | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Coquelle, N. / Brus, B. / Colletier, J.P. | |||||||||
![]() | ![]() Title: Development of an in-vivo active reversible butyrylcholinesterase inhibitor. Authors: Kosak, U. / Brus, B. / Knez, D. / Sink, R. / Zakelj, S. / Trontelj, J. / Pislar, A. / Slenc, J. / Gobec, M. / Zivin, M. / Tratnjek, L. / Perse, M. / Saat, K. / Podkowa, A. / Filipek, B. / ...Authors: Kosak, U. / Brus, B. / Knez, D. / Sink, R. / Zakelj, S. / Trontelj, J. / Pislar, A. / Slenc, J. / Gobec, M. / Zivin, M. / Tratnjek, L. / Perse, M. / Saat, K. / Podkowa, A. / Filipek, B. / Nachon, F. / Brazzolotto, X. / Wieckowska, A. / Malawska, B. / Stojan, J. / Rascan, I.M. / Kos, J. / Coquelle, N. / Colletier, J.P. / Gobec, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 438.1 KB | Display | ![]() |
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PDB format | ![]() | 360.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 44.3 KB | Display | |
Data in CIF | ![]() | 61.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dywC ![]() 5dyyC ![]() 1pomS 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59774.508 Da / Num. of mol.: 2 / Fragment: UNP rsidues 28-557 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 5 types, 16 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/FUL.gif)
![](data/chem/img/FUL.gif)
#2: Polysaccharide | #3: Polysaccharide | #4: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / #10: Sugar | ChemComp-FUL / | |
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-Non-polymers , 6 types, 250 molecules ![](data/chem/img/5HB.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-UNX / #11: Chemical | ChemComp-PEG / | #12: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2 M ammonium acetate, 12% polyethylene glycol 4000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93903 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.2 Å / Num. obs: 47153 / % possible obs: 99.99 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.0807 / Net I/σ(I): 12.48 |
Reflection shell | Resolution: 2.55→2.64 Å / Rmerge(I) obs: 0.7319 / CC1/2: 0.762 / Rrim(I) all: 0.8088 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1POM Resolution: 2.55→46.12 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.82 / 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: 2.55→46.12 Å
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Refine LS restraints |
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LS refinement shell |
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