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Yorodumi- PDB-6qab: Human Butyrylcholinesterase in complex with (S)-N-(1-((2-cyclohep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qab | |||||||||
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Title | Human Butyrylcholinesterase in complex with (S)-N-(1-((2-cycloheptylethyl)amino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-N,N-dimethylbutan-1-aminium | |||||||||
Components | Cholinesterase | |||||||||
Keywords | HYDROLASE / Butyrylcholinesterase / inhibitor / complex | |||||||||
Function / homology | Function and homology information cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / cholinesterase activity / peptide hormone processing / acetylcholinesterase activity / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | |||||||||
Authors | Brazzolotto, X. / Nachon, F. / Harst, M. / Knez, D. / Gobec, S. | |||||||||
Funding support | France, 1items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2019 Title: Tryptophan-derived butyrylcholinesterase inhibitors as promising leads against Alzheimer's disease. Authors: Meden, A. / Knez, D. / Jukic, M. / Brazzolotto, X. / Grsic, M. / Pislar, A. / Zahirovic, A. / Kos, J. / Nachon, F. / Svete, J. / Gobec, S. / Groselj, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qab.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qab.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/6qab ftp://data.pdbj.org/pub/pdb/validation_reports/qa/6qab | HTTPS FTP |
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-Related structure data
Related structure data | 6qaaC 6qacC 6qadC 6qaeC 1p0iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 63029.668 Da / Num. of mol.: 1 / Mutation: N45Q, N483Q, N509Q,N514Q, 558STOP Source method: isolated from a genetically manipulated source Details: Residues 1-20 are signal peptideNAG and FUC are glycosylationsDMS is DMSOGOL is glycerolMES is MES buffer266 is the ligand Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase |
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-Sugars , 3 types, 6 molecules
#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 | #4: Sugar | |
-Non-polymers , 6 types, 79 molecules
#5: Chemical | ChemComp-DMS / | ||||||||
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#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-MES / | #8: Chemical | ChemComp-HUQ / | #9: Chemical | ChemComp-SO4 / #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→47.58 Å / Num. obs: 27181 / % possible obs: 99.85 % / Redundancy: 8.1 % / Biso Wilson estimate: 62.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1194 / Rpim(I) all: 0.0444 / Rrim(I) all: 0.1276 / Net I/σ(I): 13.33 |
Reflection shell | Resolution: 2.49→2.579 Å / Redundancy: 8 % / Rmerge(I) obs: 1.445 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 2692 / CC1/2: 0.552 / Rpim(I) all: 0.5386 / Rrim(I) all: 1.544 / % possible all: 99.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P0I Resolution: 2.49→47.577 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.24 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→47.577 Å
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Refine LS restraints |
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LS refinement shell |
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