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Yorodumi- PDB-6t9p: Human Butyrylcholinesterase in complex with 2-(N-hydroxyimino)-N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t9p | |||||||||||||||
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Title | Human Butyrylcholinesterase in complex with 2-(N-hydroxyimino)-N-[(1R)-3-{4-[(2-methyl-1H-imidazol-1-yl)methyl]-1H-1,2,3-triazol-1-yl}-1- phenylpropyl]acetamide | |||||||||||||||
Components | Cholinesterase | |||||||||||||||
Keywords | HYDROLASE / Butyrylcholinesterase / Complex / Oxime | |||||||||||||||
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: 2.7 Å | |||||||||||||||
Authors | Brazzolotto, X. / Sinko, G. / Marakovic, N. / Knezevic, A. | |||||||||||||||
Funding support | France, 1items
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Citation | Journal: Biochem.J. / Year: 2020 Title: Enantioseparation, in vitro testing, and structural characterization of triple-binding reactivators of organophosphate-inhibited cholinesterases. Authors: Marakovic, N. / Knezevic, A. / Roncevic, I. / Brazzolotto, X. / Kovarik, Z. / Sinko, G. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t9p.cif.gz | 279.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t9p.ent.gz | 190.4 KB | Display | PDB format |
PDBx/mmJSON format | 6t9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/6t9p ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t9p | HTTPS FTP |
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-Related structure data
Related structure data | 6t9sC 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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2 |
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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 Source method: isolated from a genetically manipulated source Details: 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: (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 | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[1-deoxy-alpha-D-tagatopyranose-(2-6)]2-acetamido-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[1-deoxy-alpha-D-tagatopyranose-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1 / Source method: obtained synthetically #5: Sugar | |
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-Non-polymers , 4 types, 60 molecules
#4: Chemical | ChemComp-GOL / | ||||
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#6: Chemical | #7: Chemical | ChemComp-MXB / ( | #8: 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: 3.17 Å3/Da / Density % sol: 61.21 % |
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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: 0.97857 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→41.43 Å / Num. obs: 21379 / % possible obs: 99.88 % / Redundancy: 26.9 % / Biso Wilson estimate: 70.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1883 / Rpim(I) all: 0.03707 / Rrim(I) all: 0.1919 / Net I/σ(I): 14.41 |
Reflection shell | Resolution: 2.7→2.797 Å / Redundancy: 28.2 % / Rmerge(I) obs: 2.847 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 2100 / CC1/2: 0.601 / Rpim(I) all: 0.5427 / Rrim(I) all: 2.899 / % possible all: 99.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1p0i Resolution: 2.7→41.43 Å / SU ML: 0.442 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.604 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: 71.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→41.43 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: 137.382185566 Å / Origin y: 121.889798457 Å / Origin z: 38.6919415177 Å
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Refinement TLS group | Selection details: all |