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- PDB-2jgl: Crystal structure of mouse acetylcholinesterase inhibited by aged... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jgl | ||||||
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Title | Crystal structure of mouse acetylcholinesterase inhibited by aged VX and sarin | ||||||
![]() | ACETYLCHOLINESTERASE | ||||||
![]() | HYDROLASE / GLYCOPROTEIN / SERINE ESTERASE / ACETYLCHOLINESTERASE / ALTERNATIVE SPLICING / NEUROTRANSMITTER DEGRADATION / VX / SARIN / AGING / SYNAPSE / MEMBRANE | ||||||
Function / homology | ![]() acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nuclear envelope / presynaptic membrane / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hornberg, A. / Tunemalm, A.-K. / Ekstrom, F. | ||||||
![]() | ![]() Title: Crystal Structures of Acetylcholinesterase in Complex with Organophosphorus Compounds Suggest that the Acyl Pocket Modulates the Aging Reaction by Precluding the Formation of the Trigonal ...Title: Crystal Structures of Acetylcholinesterase in Complex with Organophosphorus Compounds Suggest that the Acyl Pocket Modulates the Aging Reaction by Precluding the Formation of the Trigonal Bipyramidal Transition State. Authors: Hornberg, A. / Tunemalm, A.-K. / Ekstrom, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.1 KB | Display | ![]() |
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PDB format | ![]() | 178.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 769 KB | Display | ![]() |
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Full document | ![]() | 783.5 KB | Display | |
Data in XML | ![]() | 42.6 KB | Display | |
Data in CIF | ![]() | 59.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jgeC ![]() 2jgfC ![]() 2jgiC ![]() 2jgjC ![]() 2jgkC ![]() 2jgmC ![]() 1j06S S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 3 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 60311.992 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 310 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/P4G.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/P4G.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-P4G / | #5: Chemical | ChemComp-P6G / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | GAP BETWEEN RESIDUES 257 AND 265 (MONOMER A AND B), STARTS AT RESIDUE 4 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68 % |
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Crystal grow | pH: 7 / Details: 28% PEG 750MME, 0.1 M HEPES PH7.0, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 28, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0863 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20.77 Å / Num. obs: 63074 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1J06 Resolution: 2.6→20.44 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.611 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). HETEROGEN: THE P6G REPRESENTS PEG750 THAT WAS USED IN CRYSTALLIZATION.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20.44 Å
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Refine LS restraints |
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