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- PDB-2xqk: X-ray Structure of human butyrylcholinesterase inhibited by pure ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xqk | |||||||||
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Title | X-ray Structure of human butyrylcholinesterase inhibited by pure enantiomer VX-(S) | |||||||||
![]() | CHOLINESTERASE | |||||||||
![]() | HYDROLASE / NERVE AGENT / BIOSCAVENGER | |||||||||
Function / homology | ![]() cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / response to folic acid / choline binding / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / response to folic acid / choline binding / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / acetylcholinesterase activity / choline metabolic process / hydrolase activity, acting on ester bonds / nuclear envelope lumen / Aspirin ADME / Synthesis of PC / Synthesis, secretion, and deacylation of Ghrelin / catalytic activity / response to glucocorticoid / xenobiotic metabolic process / learning / amyloid-beta binding / blood microparticle / negative regulation of cell population proliferation / endoplasmic reticulum lumen / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wandhammer, M. / Carletti, E. / Gillon, E. / Masson, P. / Goeldner, M. / Noort, D. / Nachon, F. | |||||||||
![]() | ![]() Title: Structural Study of the Complex Stereoselectivity of Human Butyrylcholinesterase for the Neurotoxic V-Agents. Authors: Wandhammer, M. / Carletti, E. / Van Der Schans, M. / Gillon, E. / Nicolet, Y. / Masson, P. / Goeldner, M. / Noort, D. / Nachon, 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 | ![]() | 241.4 KB | Display | ![]() |
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PDB format | ![]() | 193.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 830.9 KB | Display | ![]() |
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Full document | ![]() | 843.6 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xqfC ![]() 2xqgC ![]() 2xqiC ![]() 2xqjC ![]() 1p0iS 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59469.309 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-557 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 9 molecules ![](data/chem/img/FUC.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#10: Sugar | #11: Sugar | ChemComp-NAG / |
-Non-polymers , 9 types, 357 molecules ![](data/chem/img/GLY.gif)
![](data/chem/img/VX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/VX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GLY / | ||||||||||||
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#4: Chemical | ChemComp-VX / | ||||||||||||
#5: Chemical | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-NA / | #8: Chemical | #9: Chemical | ChemComp-K / | #12: Chemical | ChemComp-UNX / #13: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 45 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 483 TO GLN ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: AMMONIUM SULFATE 2.1 M, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID 0.1 M, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→41.5 Å / Num. obs: 30395 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.3 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P0I Resolution: 2.4→41.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.243 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 41.242 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→41.53 Å
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Refine LS restraints |
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