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Yorodumi- PDB-7xn1: Crystal structure of human acetylcholinesterase in complex with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xn1 | |||||||||
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Title | Crystal structure of human acetylcholinesterase in complex with tacrine | |||||||||
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: 2.85 Å | |||||||||
Authors | Dileep, K.V. / Ihara, K. / Mishima-Tsumagari, C. / Kukimoto-Niino, M. / Yonemochi, M. / Hanada, K. / Shirouzu, M. / Zhang, K.Y.J. | |||||||||
Funding support | Japan, 1items
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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 | 7xn1.cif.gz | 217.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xn1.ent.gz | 172.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xn1_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7xn1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7xn1_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 7xn1_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/7xn1 ftp://data.pdbj.org/pub/pdb/validation_reports/xn/7xn1 | HTTPS FTP |
-Related structure data
Related structure data | 7e3dC 7e3hC 4ey4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 59232.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: tacrine / Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 36 molecules
#4: Chemical | #5: Chemical | ChemComp-PE8 / | #6: Water | ChemComp-HOH / | |
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-Details
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: 4.3 Å3/Da / Density % sol: 71.38 % / Description: hexagonal rod like clustered crystals |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.7 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 11, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→47.02 Å / Num. obs: 48576 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.15 / Net I/σ(I): 2.6 |
Reflection shell | Resolution: 2.85→2.94 Å / Rmerge(I) obs: 0.566 / Num. unique obs: 4372 / CC1/2: 0.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EY4 Resolution: 2.85→47.02 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.5 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→47.02 Å
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Refine LS restraints |
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LS refinement shell |
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