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Yorodumi- PDB-6i0b: Human butyrylcholinesterase in complex with the S enantiomer of a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i0b | |||||||||
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Title | Human butyrylcholinesterase in complex with the S enantiomer of a chlorotacrine-tryptophan multi-target inhibitor. | |||||||||
Components | Cholinesterase | |||||||||
Keywords | HYDROLASE / butyrylcholinesterase / multi-target inhibitor | |||||||||
Function / homology | Function and homology information cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / 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 / cholinesterase activity / choline binding / response to folic acid / 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 / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.384 Å | |||||||||
Authors | Brazzolotto, X. / Nachon, F. | |||||||||
Funding support | France, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2019 Title: Novel tacrine-tryptophan hybrids: Multi-target directed ligands as potential treatment for Alzheimer's disease. Authors: Chalupova, K. / Korabecny, J. / Bartolini, M. / Monti, B. / Lamba, D. / Caliandro, R. / Pesaresi, A. / Brazzolotto, X. / Gastellier, A.J. / Nachon, F. / Pejchal, J. / Jarosova, M. / ...Authors: Chalupova, K. / Korabecny, J. / Bartolini, M. / Monti, B. / Lamba, D. / Caliandro, R. / Pesaresi, A. / Brazzolotto, X. / Gastellier, A.J. / Nachon, F. / Pejchal, J. / Jarosova, M. / Hepnarova, V. / Jun, D. / Hrabinova, M. / Dolezal, R. / Zdarova Karasova, J. / Mzik, M. / Kristofikova, Z. / Misik, J. / Muckova, L. / Jost, P. / Soukup, O. / Benkova, M. / Setnicka, V. / Habartova, L. / Chvojkova, M. / Kleteckova, L. / Vales, K. / Mezeiova, E. / Uliassi, E. / Valis, M. / Nepovimova, E. / Bolognesi, M.L. / Kuca, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i0b.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i0b.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 6i0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/6i0b ftp://data.pdbj.org/pub/pdb/validation_reports/i0/6i0b | HTTPS FTP |
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-Related structure data
Related structure data | 5nuuC 6i0cC 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: 59713.512 Da / Num. of mol.: 1 / Mutation: N17Q, N455Q, N481Q, N486Q Source method: isolated from a genetically manipulated source Details: (NAG) are N-acetylglucosamine(FUC) are fucose / 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, 124 molecules
#5: Chemical | ChemComp-MES / | ||||||
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#6: Chemical | ChemComp-9A5 / ( | ||||||
#7: Chemical | #8: Chemical | ChemComp-SO4 / #9: Chemical | ChemComp-CL / | #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: 3.1 Å3/Da / Density % sol: 60.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: MES pH 6.5 Ammonium Sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.384→55.221 Å / Num. obs: 31033 / % possible obs: 99.86 % / Redundancy: 8.2 % / Biso Wilson estimate: 50.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07364 / Rpim(I) all: 0.02706 / Rrim(I) all: 0.07865 / Net I/σ(I): 18.02 |
Reflection shell | Resolution: 2.384→2.469 Å / Redundancy: 8 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 2.56 / Num. unique obs: 3046 / CC1/2: 0.834 / Rpim(I) all: 0.2951 / Rrim(I) all: 0.8434 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1p0i Resolution: 2.384→55.221 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.384→55.221 Å
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Refine LS restraints |
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LS refinement shell |
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