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Yorodumi- PDB-5dyy: Crystal structure of human butyrylcholinesterase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dyy | |||||||||
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Title | Crystal structure of human butyrylcholinesterase in complex with N-((1-benzylpiperidin-3-yl)methyl)naphthalene-2-sulfonamide | |||||||||
Components | Cholinesterase | |||||||||
Keywords | HYDROLASE / human butyrylcholinesterase AD alzheimer disease sulfonamide | |||||||||
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 / 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: 2.65 Å | |||||||||
Authors | Coquelle, N. / Brus, B. / Colletier, J.P. | |||||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Development of an in-vivo active reversible butyrylcholinesterase inhibitor. Authors: Kosak, U. / Brus, B. / Knez, D. / Sink, R. / Zakelj, S. / Trontelj, J. / Pislar, A. / Slenc, J. / Gobec, M. / Zivin, M. / Tratnjek, L. / Perse, M. / Saat, K. / Podkowa, A. / Filipek, B. / ...Authors: Kosak, U. / Brus, B. / Knez, D. / Sink, R. / Zakelj, S. / Trontelj, J. / Pislar, A. / Slenc, J. / Gobec, M. / Zivin, M. / Tratnjek, L. / Perse, M. / Saat, K. / Podkowa, A. / Filipek, B. / Nachon, F. / Brazzolotto, X. / Wieckowska, A. / Malawska, B. / Stojan, J. / Rascan, I.M. / Kos, J. / Coquelle, N. / Colletier, J.P. / Gobec, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dyy.cif.gz | 229 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dyy.ent.gz | 188.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/5dyy ftp://data.pdbj.org/pub/pdb/validation_reports/dy/5dyy | HTTPS FTP |
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-Related structure data
Related structure data | 5dytC 5dywC 1pomS 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: 59774.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P06276, cholinesterase |
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-Sugars , 5 types, 15 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: Polysaccharide | beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 245 molecules
#6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | #9: Chemical | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM Sodium acetate 12% peg 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 10, 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: 2.65→46.21 Å / Num. obs: 42160 / % possible obs: 99.77 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.1107 / Net I/σ(I): 13.32 |
Reflection shell | Resolution: 2.65→2.745 Å / Rmerge(I) obs: 0.6709 / CC1/2: 0.803 / Rrim(I) all: 0.7272 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1POM Resolution: 2.65→46.21 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→46.21 Å
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Refine LS restraints |
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LS refinement shell |
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