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- PDB-6xta: Recombinant human butyrylcholinesterase in complex with (2S)-N-[2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xta | ||||||
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Title | Recombinant human butyrylcholinesterase in complex with (2S)-N-[2-(1-benzylazepan-4-yl)ethyl]-2-(butylamino)-3-(1H-indol-3-yl)propanamide | ||||||
![]() | Cholinesterase | ||||||
![]() | HYDROLASE / Butyrylcholinesterase / Inhibitor / Complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Brazzolotto, X. / Nachon, F. / Meden, A. / Knez, D. / Gobec, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-activity relationship study of tryptophan-based butyrylcholinesterase inhibitors. Authors: Meden, A. / Knez, D. / Malikowska-Racia, N. / Brazzolotto, X. / Nachon, F. / Svete, J. / Salat, K. / Groselj, U. / 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 | ![]() | 127.7 KB | Display | ![]() |
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PDB format | ![]() | 97.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p0iS 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59713.512 Da / Num. of mol.: 1 Mutation: N17Q, N445Q, N481Q, N486 and STOP at position 530Q Source method: isolated from a genetically manipulated source Details: Secreted protein. Signal peptide 1-28 is cleaved during secretion process. Number from the first residue Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 4 types, 6 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[1-deoxy-alpha-D-tagatopyranose-(2-6)]2-acetamido-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[1-deoxy-alpha-D-tagatopyranose-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 4 types, 60 molecules ![](data/chem/img/O0Z.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-O0Z / ( | ||||
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#7: Chemical | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.22 Å / Num. obs: 26886 / % possible obs: 99.92 % / Redundancy: 26.5 % / Biso Wilson estimate: 66.27 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1634 / Rpim(I) all: 0.03238 / Rrim(I) all: 0.1666 / Net I/σ(I): 15.64 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 27.3 % / Rmerge(I) obs: 3.048 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 2645 / CC1/2: 0.605 / CC star: 0.868 / Rpim(I) all: 0.5916 / Rrim(I) all: 3.105 / % possible all: 99.89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1p0i Resolution: 2.5→49.22 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 74.81 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→49.22 Å
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Refine LS restraints |
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