[English] 日本語
Yorodumi- PDB-5dyw: Crystal structure of human butyrylcholinesterase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dyw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human butyrylcholinesterase in complex with N-((1-benzylpiperidin-3-yl)methyl)-N-(2-methoxyethyl)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 / 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: 2.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5dyw.cif.gz | 240.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5dyw.ent.gz | 192.3 KB | Display | PDB format |
PDBx/mmJSON format | 5dyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/5dyw ftp://data.pdbj.org/pub/pdb/validation_reports/dy/5dyw | HTTPS FTP |
---|
-Related structure data
Related structure data | 5dytC 5dyyC 1pomS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59758.508 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 |
---|
-Sugars , 4 types, 15 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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 Source method: isolated from a genetically manipulated source #10: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 6 types, 310 molecules
#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-CL / #9: Chemical | ChemComp-PG4 / | #11: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.44 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2 M ammonium acetate, 12% polyethylene glycol 4000. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93903 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93903 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.2 Å / Num. obs: 45699 / % possible obs: 99.99 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.1596 / Net I/σ(I): 12.48 |
Reflection shell | Resolution: 2.55→2.589 Å / Rmerge(I) obs: 1.37 / CC1/2: 0.673 / Rrim(I) all: 1.47 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1POM Resolution: 2.5→46.016 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.36 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→46.016 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|