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- PDB-6ntn: Crystal Structure of Recombinant Human Acetylcholinesterase Inhib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ntn | |||||||||
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Title | Crystal Structure of Recombinant Human Acetylcholinesterase Inhibited by A-230 in Complex with the Reactivator, HI-6 | |||||||||
![]() | Acetylcholinesterase | |||||||||
![]() | hydrolase/hydrolase inhibitor / hydrolase / inhibitor / hydrolase-hydrolase inhibitor complex | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bester, S.M. / Guelta, M.A. / Height, J.J. / Pegan, S.D. | |||||||||
![]() | ![]() Title: Insights into inhibition of human acetylcholinesterase by Novichok, A-series Nerve Agents Authors: Height, J.J. / Bester, S.M. / Guelta, M.A. / Bae, S.Y. / Cheung, J. / Pegan, S.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 438.6 KB | Display | ![]() |
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PDB format | ![]() | 360.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ntgC ![]() 6nthC ![]() 6ntkC ![]() 6ntlC ![]() 6ntmC ![]() 6ntoC ![]() 4ey4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 462 molecules ![](data/chem/img/HI6.gif)
![](data/chem/img/L2Y.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/L2Y.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.28 Å3/Da / Density % sol: 71.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15-21% polyethylene glycol 3350 (PEG) and 0.17- 0.21M potassium nitrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.697→50 Å / Num. obs: 57260 / % possible obs: 99.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.061 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.697→2.75 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2865 / CC1/2: 0.906 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EY4 Resolution: 2.697→46.327 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.83 / 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: 2.697→46.327 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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