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Yorodumi- PDB-6wvo: Crystal Structure of Recombinant Human Acetylcholinesterase In Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wvo | ||||||
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Title | Crystal Structure of Recombinant Human Acetylcholinesterase In Complex with GD and HI-6 | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / nerve agent / acetylcholinesterase / tabun / GA | ||||||
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: 2.19 Å | ||||||
Authors | McGuire, J.R. / Bester, S.M. / Pegan, S.D. / Height, J.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chem.Res.Toxicol. / Year: 2021 Title: Structural and Biochemical Insights into the Inhibition of Human Acetylcholinesterase by G-Series Nerve Agents and Subsequent Reactivation by HI-6. Authors: McGuire, J.R. / Bester, S.M. / Guelta, M.A. / Cheung, J. / Langley, C. / Winemiller, M.D. / Bae, S.Y. / Funk, V. / Myslinski, J.M. / Pegan, S.D. / Height, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wvo.cif.gz | 292.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wvo.ent.gz | 189.8 KB | Display | PDB format |
PDBx/mmJSON format | 6wvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wvo_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 6wvo_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6wvo_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 6wvo_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/6wvo ftp://data.pdbj.org/pub/pdb/validation_reports/wv/6wvo | HTTPS FTP |
-Related structure data
Related structure data | 6wuvC 6wuyC 6wuzC 6wv1C 6wvcC 6wvpC 6wvqC 4ey4S C: citing same article (ref.) 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: 59447.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 6 types, 524 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #7: Chemical | ChemComp-NO3 / | #8: Chemical | ChemComp-PE8 / | #9: 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 % sol: 71.46 % / Mosaicity: 0.432 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, KNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.193→200 Å / Num. obs: 106415 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 42.63 Å2 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.075 / Rrim(I) all: 0.23 / Χ2: 1.01 / Net I/σ(I): 3.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EY4 Resolution: 2.19→49.87 Å / SU ML: 0.3233 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.6184 / Stereochemistry target values: 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: 46.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→49.87 Å
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Refine LS restraints |
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LS refinement shell |
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