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Yorodumi- PDB-6rua: Structure of recombinant human butyrylcholinesterase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rua | |||||||||
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Title | Structure of recombinant human butyrylcholinesterase in complex with a coumarin-based fluorescent probe linked to sulfonamide type inhibitor. | |||||||||
Components | Cholinesterase | |||||||||
Keywords | HYDROLASE / human butyrylcholinesterase / insect cell / fluorescent probes / sulfonamide / 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: 2.75 Å | |||||||||
Authors | Coquelle, N. / Knez, D. / Brus, B. / Gobec, S. / Colletier, J.P. | |||||||||
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 | 6rua.cif.gz | 238.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rua.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 6rua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/6rua ftp://data.pdbj.org/pub/pdb/validation_reports/ru/6rua | HTTPS FTP |
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-Related structure data
Related structure data | 6r6vC 6r6wC 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, 2 molecules AB
#1: Protein | Mass: 65149.500 Da / Num. of mol.: 2 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, 15 molecules
#2: Polysaccharide | #3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 192 molecules
#7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-CL / #9: Chemical | ChemComp-PEG / | #10: Chemical | ChemComp-KJT / | #11: Chemical | ChemComp-PGE / | #12: Water | ChemComp-HOH / | |
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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: 2.98 Å3/Da / Density % sol: 58.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M ammonium acetate 12% PEG 4000 pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→44.93 Å / Num. obs: 37475 / % possible obs: 99.1 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09612 / Net I/σ(I): 12.71 |
Reflection shell | Resolution: 2.75→2.848 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.6969 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 3702 / CC1/2: 0.746 / % possible all: 99.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P0I Resolution: 2.75→44.927 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→44.927 Å
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Refine LS restraints |
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LS refinement shell |
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