[English] 日本語
Yorodumi- PDB-7qbr: Human butyrylcholinesterase in complex with (Z)-N-tert-butyl-1-(8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qbr | ||||||
---|---|---|---|---|---|---|---|
Title | Human butyrylcholinesterase in complex with (Z)-N-tert-butyl-1-(8-(3-(4-(prop-2-yn-1-yl)piperazin-1-yl)propoxy)quinolin-2-yl)methanimine oxide | ||||||
Components | Cholinesterase | ||||||
Keywords | HYDROLASE / Butyrylcholinesterase / Inhibitor / Complex | ||||||
Function / homology | Function and homology information cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / acetylcholine catabolic process / response to alkaloid / peptide hormone processing ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / acetylcholine catabolic process / response to alkaloid / peptide hormone processing / negative regulation of synaptic transmission / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Denic, M. / Chioua, M. / Knez, D. / Gobec, S. / Nachon, F. / Marco-Contelles, J.L. / Brazzolotto, X. | ||||||
Funding support | France, 1items
| ||||||
Citation | Journal: Acta Pharm Sin B / Year: 2023 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qbr.cif.gz | 290.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qbr.ent.gz | 197 KB | Display | PDB format |
PDBx/mmJSON format | 7qbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qbr_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qbr_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7qbr_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 7qbr_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/7qbr ftp://data.pdbj.org/pub/pdb/validation_reports/qb/7qbr | HTTPS FTP |
-Related structure data
Related structure data | 7qbqC 7zpbC 7zw3C 1p0iS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-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.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase |
---|
-Sugars , 4 types, 7 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | #7: Sugar | ChemComp-SIA / | |
---|
-Non-polymers , 6 types, 227 molecules
#4: Chemical | #6: Chemical | ChemComp-AI6 / | #8: Chemical | ChemComp-MES / | #9: Chemical | ChemComp-CL / #10: Chemical | ChemComp-SO4 / #11: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.63 % |
---|---|
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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 15, 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: 2.13→49.7 Å / Num. obs: 44313 / % possible obs: 98.98 % / Redundancy: 9.35 % / Biso Wilson estimate: 48.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1378 / Rpim(I) all: 0.04855 / Rrim(I) all: 0.1467 / Net I/σ(I): 9.35 |
Reflection shell | Resolution: 2.13→2.206 Å / Redundancy: 8.8 % / Rmerge(I) obs: 2.409 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4113 / CC1/2: 0.384 / Rpim(I) all: 0.8273 / Rrim(I) all: 2.5557 / % possible all: 93.39 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1p0i Resolution: 2.13→49.7 Å / SU ML: 0.2687 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8286 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: 60.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→49.7 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 139.226904815 Å / Origin y: 123.639843429 Å / Origin z: 38.8262785233 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: chain 'A' |