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- PDB-4b0p: Crystal structure of soman-aged human butyrylcholinesterase in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b0p | |||||||||
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Title | Crystal structure of soman-aged human butyrylcholinesterase in complex with methyl 2-(pentafluorobenzyloxyimino)pyridinium | |||||||||
![]() | CHOLINESTERASE | |||||||||
![]() | HYDROLASE / AGING | |||||||||
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. / de Koning, M. / van Grol, M. / Noort, D. / Goeldner, M. / Nachon, F. | |||||||||
![]() | ![]() Title: A Step Toward the Reactivation of Aged Cholinesterases -Crystal Structure of Ligands Binding to Aged Human Butyrylcholinesterase Authors: Wandhammer, M. / De Koning, M. / Van Grol, M. / Loiodice, M. / Saurel, L. / Noort, D. / Goeldner, M. / 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 | ![]() | 237.2 KB | Display | ![]() |
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PDB format | ![]() | 190 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4axbC ![]() 4b0oC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59791.512 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-557 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 #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 7 types, 201 molecules ![](data/chem/img/GLY.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MF5.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MF5.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GLY / | ||||||||||
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#4: Chemical | #5: Chemical | ChemComp-K / | #6: Chemical | ChemComp-MF5 / | #8: Chemical | ChemComp-CA / #9: Chemical | ChemComp-CL / #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 2.1 M AMMONIUM SULFATE, 0.1 M MES BUFFER PH 6.5 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00407 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30.88 Å / Num. obs: 27807 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 3.58 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P0I Resolution: 2.5→30.878 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 22.85 / 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 / Bsol: 58.98 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30.878 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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