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Yorodumi- PDB-8dt5: X-ray structure of human acetylcholinesterase ternary complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dt5 | ||||||
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Title | X-ray structure of human acetylcholinesterase ternary complex with paraoxon and oxime RS170B (POX-hAChE-RS170B) | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / acetylcholine hydrolysis / oxime reactivator | ||||||
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: 2.6 Å | ||||||
Authors | Kovalevsky, A.Y. / Gerlits, O. / Radic, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2022 Title: Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering. Authors: Gerlits, O. / Fajer, M. / Cheng, X. / Blumenthal, D.K. / Radic, Z. / Kovalevsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dt5.cif.gz | 227.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dt5.ent.gz | 181 KB | Display | PDB format |
PDBx/mmJSON format | 8dt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dt5_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8dt5_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8dt5_validation.xml.gz | 41 KB | Display | |
Data in CIF | 8dt5_validation.cif.gz | 57.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/8dt5 ftp://data.pdbj.org/pub/pdb/validation_reports/dt/8dt5 | HTTPS FTP |
-Related structure data
Related structure data | 8dt2C 8dt4C 8dt7C 6u34S 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
#1: Protein | Mass: 60287.977 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: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: 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 grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES, pH 7.5, 20 mM sodium citrate, and 7-8.5 % PEG6000 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 66518 / % possible obs: 95.4 % / Redundancy: 2.6 % / CC1/2: 0.971 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2 / Num. unique obs: 6738 / CC1/2: 0.475 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6U34 Resolution: 2.6→38.921 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 23.06 / 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: 2.6→38.921 Å
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Refine LS restraints |
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LS refinement shell |
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