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Yorodumi- PDB-6zwi: Human butyrylcholinesterase in complex with ((6-((2E,4E)-5-(benzo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zwi | ||||||
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Title | Human butyrylcholinesterase in complex with ((6-((2E,4E)-5-(benzo[d][1,3]dioxol-5-yl)penta-2,4-dienamido)hexyl)triphenylphosphonium bromide) | ||||||
Components | Cholinesterase | ||||||
Keywords | HYDROLASE / Butyrylcholinesterase / inhibitor / mitochondria | ||||||
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: 1.85 Å | ||||||
Authors | Da Silva, O. / Nachon, F. / Dias, J. / Brazzolotto, X. | ||||||
Citation | Journal: Antioxidants (Basel) / Year: 2021 Title: Fine-Tuning the Biological Profile of Multitarget Mitochondriotropic Antioxidants for Neurodegenerative Diseases. Authors: Chavarria, D. / Da Silva, O. / Benfeito, S. / Barreiro, S. / Garrido, J. / Cagide, F. / Soares, P. / Remiao, F. / Brazzolotto, X. / Nachon, F. / Oliveira, P.J. / Dias, J. / Borges, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zwi.cif.gz | 165.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zwi.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/6zwi ftp://data.pdbj.org/pub/pdb/validation_reports/zw/6zwi | HTTPS FTP |
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-Related structure data
Related structure data | 6zweC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59713.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase |
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-Sugars , 5 types, 7 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-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 | ||
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#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source | ||
#4: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | |
-Non-polymers , 7 types, 241 molecules
#7: Chemical | ChemComp-GOL / | ||||||
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#8: Chemical | ChemComp-QRH / ( | ||||||
#9: Chemical | ChemComp-LEA / | ||||||
#10: Chemical | ChemComp-CL / #11: Chemical | ChemComp-SO4 / #12: Chemical | #13: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Ammonium sulfate, 2-(N-Morpholino)-ethanesulfonic acid, pH 6.5, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.79 Å / Num. obs: 65496 / % possible obs: 99.96 % / Redundancy: 51.4 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1014 / Net I/σ(I): 29.97 |
Reflection shell | Resolution: 1.85→1.916 Å / Num. unique obs: 6485 / CC1/2: 0.31 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P0I Resolution: 1.85→48.79 Å / SU ML: 0.2935 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0604 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: 56.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→48.79 Å
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Refine LS restraints |
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LS refinement shell |
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