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- PDB-7p1n: Crystal structure of human acetylcholinesterase in complex with (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p1n | ||||||
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Title | Crystal structure of human acetylcholinesterase in complex with (2R,3R,4S,5S,6R)-2-{4-[1-(4-{5-hydroxy-6-[(E)-(hydroxyimino)methyl]pyridin-2-yl}butyl)-1H-1,2,3-triazol-4-yl]butoxy}-6-(hydroxymethyl)oxane-3,4,5-triol oxime | ||||||
![]() | (Acetylcholinesterase) x 2 | ||||||
![]() | HYDROLASE / cholinesterase / glucoconjugated oximes | ||||||
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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Da Silva, O. / Dias, J. / Nachon, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A New Class of Bi- and Trifunctional Sugar Oximes as Antidotes against Organophosphorus Poisoning. Authors: Da Silva, O. / Probst, N. / Landry, C. / Hanak, A.S. / Warnault, P. / Coisne, C. / Calas, A.G. / Gosselet, F. / Courageux, C. / Gastellier, A.J. / Trancart, M. / Baati, R. / Dehouck, M.P. / ...Authors: Da Silva, O. / Probst, N. / Landry, C. / Hanak, A.S. / Warnault, P. / Coisne, C. / Calas, A.G. / Gosselet, F. / Courageux, C. / Gastellier, A.J. / Trancart, M. / Baati, R. / Dehouck, M.P. / Jean, L. / Nachon, F. / Renard, P.Y. / Dias, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 535.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 42.9 KB | Display | |
Data in CIF | ![]() | 60.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p1pC ![]() 4ey4S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 , 2 types, 4 molecules aabbAB
#1: Protein | Mass: 27775.518 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 31478.549 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 3 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-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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#4: 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 |
#5: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
-Non-polymers , 6 types, 258 molecules ![](data/chem/img/4J1.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-CL / #9: Chemical | ChemComp-GOL / | #10: Chemical | ChemComp-MG / #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.25 Å3/Da / Density % sol: 80.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M LiSO4, 100 mM HEPES pH7, 60 mM MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→78.33 Å / Num. obs: 62748 / % possible obs: 99.92 % / Redundancy: 7.6 % / Biso Wilson estimate: 71.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09202 / Net I/σ(I): 16.27 |
Reflection shell | Resolution: 2.95→3.055 Å / Rmerge(I) obs: 0.6054 / Mean I/σ(I) obs: 2.85 / Num. measured obs: 48332 / Num. unique obs: 6237 / CC1/2: 0.915 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EY4 Resolution: 2.95→78.33 Å / SU ML: 0.3314 / Cross valid method: FREE R-VALUE / Phase error: 24.4595 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: 83.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→78.33 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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