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Yorodumi- PDB-7q1n: Crystal structure of human butyrylcholinesterase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q1n | |||||||||
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Title | Crystal structure of human butyrylcholinesterase in complex with N-[(2R)-3-[(cyclohexylmethyl)amino]-2-hydroxypropyl]-2,2-diphenylacetamide | |||||||||
Components | Cholinesterase | |||||||||
Keywords | HYDROLASE / Butyrylcholinesterase / Inhibitor / Complex | |||||||||
Function / homology | Function and homology information cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / response to alkaloid / choline binding / response to folic acid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / response to alkaloid / choline binding / response to folic acid / 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 / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Brazzolotto, X. / Panek, D. / Pasieka, A. / Malawska, B. / Nachon, F. | |||||||||
Funding support | France, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2023 Title: Discovery of new, highly potent and selective inhibitors of BuChE - design, synthesis, in vitro and in vivo evaluation and crystallography studies. Authors: Panek, D. / Pasieka, A. / Latacz, G. / Zareba, P. / Szczech, M. / Godyn, J. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Walczak, M. / Smolik, M. / Salat, K. ...Authors: Panek, D. / Pasieka, A. / Latacz, G. / Zareba, P. / Szczech, M. / Godyn, J. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Walczak, M. / Smolik, M. / Salat, K. / Hofner, G. / Wanner, K. / Wieckowska, A. / Malawska, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q1n.cif.gz | 289.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q1n.ent.gz | 196.4 KB | Display | PDB format |
PDBx/mmJSON format | 7q1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/7q1n ftp://data.pdbj.org/pub/pdb/validation_reports/q1/7q1n | HTTPS FTP |
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-Related structure data
Related structure data | 7q1mC 7q1oC 7q1pC 1p0iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 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.) 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 | Source method: isolated from a genetically manipulated source #5: Sugar | |
-Non-polymers , 7 types, 172 molecules
#4: Chemical | ChemComp-8IV / | ||||||||||
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#6: Chemical | #7: Chemical | ChemComp-GOA / | #8: Chemical | #9: Chemical | ChemComp-CL / #10: Chemical | #11: 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: 61.37 % |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.354→109.1 Å / Num. obs: 31957 / % possible obs: 99.12 % / Redundancy: 26.8 % / Biso Wilson estimate: 58.61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1635 / Rpim(I) all: 0.03226 / Rrim(I) all: 0.1667 / Net I/σ(I): 14.06 |
Reflection shell | Resolution: 2.354→2.438 Å / Redundancy: 25.2 % / Rmerge(I) obs: 2.438 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 2942 / CC1/2: 0.615 / Rpim(I) all: 0.4791 / Rrim(I) all: 2.486 / % possible all: 91.56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1p0i Resolution: 2.35→109.1 Å / SU ML: 0.2953 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.2247 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: 73.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→109.1 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: 16.8681108024 Å / Origin y: 32.1367068534 Å / Origin z: 38.6568978787 Å
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Refinement TLS group | Selection details: chain A |