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Yorodumi- PDB-6f25: Crystal structure of human acetylcholinesterase in complex with C35. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f25 | |||||||||
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Title | Crystal structure of human acetylcholinesterase in complex with C35. | |||||||||
Components | Acetylcholinesterase | |||||||||
Keywords | HYDROLASE / Acetylcholinesterase | |||||||||
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 / acetylcholinesterase / amyloid precursor protein metabolic process / 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 / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / side of membrane / synaptic cleft / laminin binding / collagen binding / synapse assembly / 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 / cell adhesion / hydrolase activity / 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: 3.05199647812 Å | |||||||||
Authors | Dias, J. / Nachon, F. | |||||||||
Funding support | France, 1items
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Citation | Journal: Neuropharmacology / Year: 2019 Title: New evidence for dual binding site inhibitors of acetylcholinesterase as improved drugs for treatment of Alzheimer's disease. Authors: Zueva, I. / Dias, J. / Lushchekina, S. / Semenov, V. / Mukhamedyarov, M. / Pashirova, T. / Babaev, V. / Nachon, F. / Petrova, N. / Nurullin, L. / Zakharova, L. / Ilyin, V. / Masson, P. / Petrov, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f25.cif.gz | 283.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f25.ent.gz | 185.2 KB | Display | PDB format |
PDBx/mmJSON format | 6f25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/6f25 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/6f25 | HTTPS FTP |
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-Related structure data
Related structure data | 3liiS S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59103.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22303, acetylcholinesterase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 248 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-CL / #8: Water | ChemComp-HOH / | |
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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: 6.33 Å3/Da / Density % sol: 80.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.5 M LiSo4, 100 mM Hepes pH 7, 60 mM MgSo4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→48.89 Å / Num. obs: 55240 / % possible obs: 98.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 78.548294483 Å2 / Rmerge(I) obs: 0.05284 / Rrim(I) all: 0.07473 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 3.05→3.16 Å / Rmerge(I) obs: 0.6606 / Rrim(I) all: 0.9343 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LII Resolution: 3.05199647812→48.8888375148 Å / SU ML: 0.413789398865 / Cross valid method: FREE R-VALUE / σ(F): 1.33784247226 / Phase error: 23.6314281526 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: 80.7123371356 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05199647812→48.8888375148 Å
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Refine LS restraints |
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LS refinement shell |
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