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Yorodumi- PDB-6r6v: Structure of recombinant human butyrylcholinesterase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r6v | |||||||||
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Title | Structure of recombinant human butyrylcholinesterase in complex with a fluorescent coumarin-based probe | |||||||||
Components | Cholinesterase | |||||||||
Keywords | HYDROLASE / Butyrylcholinesterase / protein-ligand complex / fluorescent probe | |||||||||
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: 2.5 Å | |||||||||
Authors | Brazzolotto, X. / Nachon, F. / Knez, D. / Gobec, S. | |||||||||
Funding support | France, 1items
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Citation | Journal: J Enzyme Inhib Med Chem / Year: 2020 Title: Development of potent reversible selective inhibitors of butyrylcholinesterase as fluorescent probes. Authors: Pajk, S. / Knez, D. / Kosak, U. / Zorovic, M. / Brazzolotto, X. / Coquelle, N. / Nachon, F. / Colletier, J.P. / Zivin, M. / Stojan, J. / Gobec, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r6v.cif.gz | 130.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r6v.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 6r6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/6r6v ftp://data.pdbj.org/pub/pdb/validation_reports/r6/6r6v | HTTPS FTP |
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-Related structure data
Related structure data | 6r6wC 6ruaC 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: 59354.223 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 , 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 #4: Sugar | |
-Non-polymers , 3 types, 177 molecules
#5: Chemical | ChemComp-JU5 / ~{ | ||
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#6: Chemical | ChemComp-SO4 / #7: 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: 3.24 Å3/Da / Density % sol: 61.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.9 Å / Num. obs: 27001 / % possible obs: 98.95 % / Redundancy: 6.5 % / Biso Wilson estimate: 56.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07755 / Rpim(I) all: 0.03107 / Rrim(I) all: 0.08423 / Net I/σ(I): 14.58 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.6376 / Mean I/σ(I) obs: 2.55 / Num. unique obs: 2689 / CC1/2: 0.823 / Rpim(I) all: 0.2458 / Rrim(I) all: 0.6882 / % possible all: 99.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P0I Resolution: 2.5→47.894 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.41 Å2 / Biso mean: 62.179 Å2 / Biso min: 30.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→47.894 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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