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- PDB-6r6w: Structure of recombinant human butyrylcholinesterase in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r6w | |||||||||
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Title | Structure of recombinant human butyrylcholinesterase in complex with a fluorescent NBD-based probe | |||||||||
![]() | Cholinesterase | |||||||||
![]() | HYDROLASE / Butyrylcholinesterase / protein-ligand complex / fluorescent probe | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Brazzolotto, X. / Nachon, F. / Knez, D. / Gobec, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Development of potent reversible selective inhibitors of butyrylcholinesterase as fluorescent probes. Authors: Pajk, S. / Knez, D. / Kosak, U. / Zorovic, M. / Brazzolotto, X. / Coquelle, N. / Nachon, F. / Colletier, J.P. / Zivin, M. / Stojan, J. / Gobec, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.3 KB | Display | ![]() |
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PDB format | ![]() | 98.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6r6vC ![]() 6ruaC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59354.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
-Non-polymers , 5 types, 99 molecules ![](data/chem/img/JUB.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-JUB / [ | ||||
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#6: Chemical | ChemComp-GOL / | ||||
#7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-DMS / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972422 Å / Relative weight: 1 |
Reflection | Resolution: 2.474→60.7 Å / Num. obs: 26287 / % possible obs: 94.63 % / Redundancy: 7.6 % / Biso Wilson estimate: 60.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07009 / Rpim(I) all: 0.02689 / Rrim(I) all: 0.07524 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.474→2.562 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.9361 / Num. unique obs: 2723 / CC1/2: 0.758 / Rpim(I) all: 0.3458 / Rrim(I) all: 0.9993 / % possible all: 99.96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P0I Resolution: 2.474→60.7 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.74 Å2 / Biso mean: 66.7131 Å2 / Biso min: 35.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.474→60.7 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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