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- PDB-2xqi: X-ray Structure of human butyrylcholinesterase inhibited by racem... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xqi | |||||||||
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Title | X-ray Structure of human butyrylcholinesterase inhibited by racemic CVX | |||||||||
![]() | 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 / choline metabolic process / hydrolase activity, acting on ester bonds / acetylcholinesterase activity / Aspirin ADME / nuclear envelope lumen / 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 | ![]() | 239.2 KB | Display | ![]() |
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PDB format | ![]() | 191.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xqfC ![]() 2xqgC ![]() 2xqjC ![]() 2xqkC ![]() 1p0iS 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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Unit cell |
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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 , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 7 types, 282 molecules ![](data/chem/img/GLY.gif)
![](data/chem/img/CVX.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CVX.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GLY / | ||||||||
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#4: Chemical | ChemComp-CVX / | ||||||||
#5: Chemical | #6: Chemical | #7: Chemical | #9: Chemical | ChemComp-UNX / #10: Water | ChemComp-HOH / | |
-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: 6.6 Details: AMMONIUM SULFATE 2.1 M, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID 0.1 M, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.1 Å / Num. obs: 23438 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.6→2.9 Å / Redundancy: 9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.12 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P0I Resolution: 2.6→49.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 20.411 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.574 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUMMY ATOMS (UNX RESIDUES, ELEMENT X) WERE MODELLED WITH THE SCATTERING FACTOR FOR OXYGEN.
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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: 53.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→49.06 Å
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Refine LS restraints |
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