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Yorodumi- PDB-7e3h: Crystal structure of human acetylcholinesterase in complex with d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e3h | ||||||
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Title | Crystal structure of human acetylcholinesterase in complex with donepezil | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / Human acetylcholinesterase / hAChE / Alzheimer's disease | ||||||
Function / homology | Function and homology information negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / choline metabolic process / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Dileep, K.V. / Ihara, K. / Mishima-Tsumagari, C. / Kukimoto-Niino, M. / Yonemochi, M. / Hanada, K. / Shirouzu, M. / Zhang, K.Y.J. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2022 Title: Crystal structure of human acetylcholinesterase in complex with tacrine: Implications for drug discovery Authors: Dileep, K. / Ihara, K. / Mishima-Tsumagari, C. / Kukimoto-Niino, M. / Yonemochi, M. / Hanada, K. / Shirouzu, M. / Zhang, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e3h.cif.gz | 218.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e3h.ent.gz | 173.1 KB | Display | PDB format |
PDBx/mmJSON format | 7e3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e3h_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7e3h_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7e3h_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 7e3h_validation.cif.gz | 51 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/7e3h ftp://data.pdbj.org/pub/pdb/validation_reports/e3/7e3h | HTTPS FTP |
-Related structure data
Related structure data | 7e3dC 7xn1C 4ey7S 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: 59232.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: 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: 4.34 Å3/Da / Density % sol: 71.63 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100 mM Tris HCl buffer pH 9.0, 20 % PEG 3350, 200 mM KNO3 PH range: 8.0 - 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 18, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.45→47.2 Å / Num. obs: 77020 / % possible obs: 100 % / Redundancy: 22.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Net I/σ(I): 23.9 / Num. measured all: 1708002 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EY7 Resolution: 2.45→47.2 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.01 / 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: 116.2 Å2 / Biso mean: 41.2213 Å2 / Biso min: 21.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.45→47.2 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28 / % reflection obs: 100 %
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