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- PDB-7qbq: Human butyrylcholinesterase in complex with (Z)-N-benzyl-1-(8-hyd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qbq | ||||||
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Title | Human butyrylcholinesterase in complex with (Z)-N-benzyl-1-(8-hydroxyquinolin-2-yl)methanimine oxide | ||||||
![]() | Cholinesterase | ||||||
![]() | HYDROLASE / Butyrylcholinesterase / Inhibitor / Complex | ||||||
Function / homology | ![]() cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / 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 / 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 | ![]() ![]() ![]() | ||||||
![]() | Denic, M. / Chioua, M. / Knez, D. / Gobec, S. / Nachon, F. / Marco-Contelles, J.L. / Brazzolotto, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 8-Hydroxyquinolylnitrones as multifunctional ligands for the therapy of neurodegenerative diseases. Authors: Knez, D. / Diez-Iriepa, D. / Chioua, M. / Gottinger, A. / Denic, M. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Meden, A. / Pislar, A. / Kos, J. / Zakelj, S. ...Authors: Knez, D. / Diez-Iriepa, D. / Chioua, M. / Gottinger, A. / Denic, M. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Meden, A. / Pislar, A. / Kos, J. / Zakelj, S. / Stojan, J. / Salat, K. / Serrano, J. / Fernandez, A.P. / Sanchez-Garcia, A. / Martinez-Murillo, R. / Binda, C. / Lopez-Munoz, F. / Gobec, S. / Marco-Contelles, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 282.5 KB | Display | ![]() |
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PDB format | ![]() | 191.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qbrC ![]() 7zpbC ![]() 7zw3C ![]() 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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1 |
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Unit cell |
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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 | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 4 types, 101 molecules ![](data/chem/img/AI0.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | #8: 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: 3.18 Å3/Da / Density % sol: 61.35 % |
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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 EIGER2 X 16M / Detector: PIXEL / Date: Apr 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→41.46 Å / Num. obs: 26212 / % possible obs: 96.61 % / Redundancy: 8.2 % / Biso Wilson estimate: 57.54 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1213 / Rpim(I) all: 0.04371 / Rrim(I) all: 0.1296 / Net I/σ(I): 8.97 |
Reflection shell | Resolution: 2.49→2.584 Å / Rmerge(I) obs: 1.258 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 2514 / CC1/2: 0.439 / Rpim(I) all: 0.4633 / Rrim(I) all: 1.347 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1p0i Resolution: 2.49→41.46 Å / SU ML: 0.3272 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4734 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: 68.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→41.46 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: 16.7528459355 Å / Origin y: 32.3104967236 Å / Origin z: 38.5553139496 Å
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Refinement TLS group | Selection details: chain 'A' |