[English] 日本語
![](img/lk-miru.gif)
- PDB-7bo4: Human Butyrylcholinesterase in complex with 3-(2-(butyl(2-cyclohe... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7bo4 | ||||||
---|---|---|---|---|---|---|---|
Title | Human Butyrylcholinesterase in complex with 3-(2-(butyl(2-cycloheptylethyl)amino)ethyl)-1H-indol-6-ol | ||||||
![]() | Cholinesterase | ||||||
![]() | HYDROLASE / Butyrylcholinesterase / Complex / Inhibitor | ||||||
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. / Meden, A. / Knez, D. / Nachon, F. / Gobec, S. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: From tryptophan-based amides to tertiary amines: Optimization of a butyrylcholinesterase inhibitor series. Authors: Meden, A. / Knez, D. / Brazzolotto, X. / Nachon, F. / Dias, J. / Svete, J. / Stojan, J. / Groselj, U. / Gobec, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 280.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 190.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7bo3C ![]() 1p0iS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() |
---|
-Sugars , 4 types, 7 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/SIA.gif)
![](data/chem/img/SIA.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / | #8: Sugar | ChemComp-SIA / | |
---|
-Non-polymers , 5 types, 102 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/A87.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/A87.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MES / | ||
---|---|---|---|
#6: Chemical | ChemComp-MOH / | ||
#7: Chemical | ChemComp-A87 / | ||
#9: Chemical | ChemComp-SO4 / #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.41 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.401→49.4 Å / Num. obs: 30671 / % possible obs: 99.58 % / Redundancy: 26.9 % / Biso Wilson estimate: 57.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1548 / Rpim(I) all: 0.03031 / Rrim(I) all: 0.1578 / Net I/σ(I): 16.51 |
Reflection shell | Resolution: 2.401→2.487 Å / Rmerge(I) obs: 2.179 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 2922 / CC1/2: 0.637 / Rpim(I) all: 0.4271 / Rrim(I) all: 2.222 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1p0i Resolution: 2.401→49.4 Å / SU ML: 0.305 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9866 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.401→49.4 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
|