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- PDB-9gcq: Human Butyrylcholinesterase in complex with N1,N1-dimethyl-N2-(6-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9gcq | ||||||
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Title | Human Butyrylcholinesterase in complex with N1,N1-dimethyl-N2-(6-(naphthalen-2-yl)-5-(pyridin-4-yl)pyridazin-3-yl)ethane-1,2-diamine | ||||||
![]() | Cholinesterase | ||||||
![]() | HYDROLASE / Butyrylcholinesterase / inhibitor / complex | ||||||
Function / homology | ![]() cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / response to alkaloid / choline metabolic process / acetylcholine catabolic process ...cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / response to alkaloid / choline metabolic process / acetylcholine catabolic process / negative regulation of synaptic transmission / hydrolase activity, acting on ester bonds / peptide hormone processing / acetylcholinesterase activity / nuclear envelope lumen / Synthesis of PC / Aspirin ADME / catalytic activity / Synthesis, secretion, and deacylation of Ghrelin / xenobiotic metabolic process / response to glucocorticoid / learning / amyloid-beta binding / blood microparticle / endoplasmic reticulum lumen / negative regulation of cell population proliferation / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brazzolotto, X. / Meden, A. / Knez, D. / Gobec, S. / Nachon, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Human Butyrylcholinesterase in complex with N1,N1-dimethyl-N2-(6-(naphthalen-2-yl)-5-(pyridin-4-yl)pyridazin-3-yl)ethane-1,2-diamine Authors: Brazzolotto, X. / Meden, A. / Knez, D. / Gobec, S. / 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 | ![]() | 277.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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: 59713.512 Da / Num. of mol.: 1 Mutation: N17Q, N455Q, N481Q, N486Q mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 6 molecules 
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 4 types, 93 molecules 




#5: Chemical | ChemComp-A1IKC / Mass: 369.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23N5 | ||
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#6: Chemical | ChemComp-MES / | ||
#7: Chemical | ChemComp-SO4 / #8: Water | ChemComp-HOH / | |
-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.4 % |
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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 9M / Detector: PIXEL / Date: Dec 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→48.93 Å / Num. obs: 23190 / % possible obs: 99.11 % / Redundancy: 14 % / Biso Wilson estimate: 60.32 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1392 / Rpim(I) all: 0.03835 / Rrim(I) all: 0.1444 / Net I/σ(I): 14.13 |
Reflection shell | Resolution: 2.62→2.74 Å / Redundancy: 13 % / Rmerge(I) obs: 1.57 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 5101 / CC1/2: 0.72 / CC star: 0.915 / Rpim(I) all: 0.4397 / Rrim(I) all: 1.631 / % possible all: 93.02 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→48.93 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.6792726797 Å / Origin y: 32.0403138757 Å / Origin z: 38.6269890085 Å
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Refinement TLS group | Selection details: chain 'A' and (resid 3 through 529) |