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Yorodumi- PDB-7aiv: Crystal structure of Torpedo Californica acetylcholinesterase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aiv | ||||||
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Title | Crystal structure of Torpedo Californica acetylcholinesterase in complex with 4-{[(3-Chloro-6,7,10,11-tetrahydro-9-methyl-7,11-methanocycloocta[b]quinolin-12-yl)amino]methyl}-N-(4-hydroxy-3-methoxybenzyl)benzamide | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / Torpedo Californica acetylcholinesterase / AD / alzheimer disease | ||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / choline metabolic process / acetylcholinesterase activity / side of membrane / synaptic cleft / synapse / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Tetronarce californica (Pacific electric ray) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Coquelle, N. / Colletier, J.P. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of a Potent Dual Inhibitor of Acetylcholinesterase and Butyrylcholinesterase with Antioxidant Activity that Alleviates Alzheimer-like Pathology in Old APP/PS1 Mice. Authors: Viayna, E. / Coquelle, N. / Cieslikiewicz-Bouet, M. / Cisternas, P. / Oliva, C.A. / Sanchez-Lopez, E. / Ettcheto, M. / Bartolini, M. / De Simone, A. / Ricchini, M. / Rendina, M. / Pons, M. / ...Authors: Viayna, E. / Coquelle, N. / Cieslikiewicz-Bouet, M. / Cisternas, P. / Oliva, C.A. / Sanchez-Lopez, E. / Ettcheto, M. / Bartolini, M. / De Simone, A. / Ricchini, M. / Rendina, M. / Pons, M. / Firuzi, O. / Perez, B. / Saso, L. / Andrisano, V. / Nachon, F. / Brazzolotto, X. / Garcia, M.L. / Camins, A. / Silman, I. / Jean, L. / Inestrosa, N.C. / Colletier, J.P. / Renard, P.Y. / Munoz-Torrero, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aiv.cif.gz | 231 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aiv.ent.gz | 182.7 KB | Display | PDB format |
PDBx/mmJSON format | 7aiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aiv_validation.pdf.gz | 716.8 KB | Display | wwPDB validaton report |
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Full document | 7aiv_full_validation.pdf.gz | 724.8 KB | Display | |
Data in XML | 7aiv_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 7aiv_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/7aiv ftp://data.pdbj.org/pub/pdb/validation_reports/ai/7aiv | HTTPS FTP |
-Related structure data
Related structure data | 7aisC 7aitC 7aiuC 7aiwC 7aixC 7aiyC 2xi4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 65970.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Tetronarce californica (Pacific electric ray) References: UniProt: P04058, acetylcholinesterase #2: Chemical | ChemComp-8UE / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 50 mM MES 28-32% PEG 200 / PH range: 5.8-6.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 48442 / % possible obs: 98.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 41.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.55→2.62 Å / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 11815 / CC1/2: 0.807 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2xi4 Resolution: 2.55→19.984 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.1 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.68 Å2 / Biso mean: 38.0157 Å2 / Biso min: 14.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→19.984 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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