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Yorodumi- PDB-2wsl: Aged Form of Human Butyrylcholinesterase Inhibited by Tabun Analo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wsl | |||||||||
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Title | Aged Form of Human Butyrylcholinesterase Inhibited by Tabun Analogue TA4 | |||||||||
Components | CHOLINESTERASE | |||||||||
Keywords | HYDROLASE / TABUN / AGING / INHIBITION / BUTYRYLCHOLINESTERASE / GLYCOPROTEIN / SERINE ESTERASE / DISEASE MUTATION | |||||||||
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 Å | |||||||||
Authors | Carletti, E. / Aurbek, N. / Gillon, E. / Loiodice, M. / Nicolet, Y. / Fontecilla, J. / Masson, P. / Thiermann, H. / Nachon, F. / Worek, F. | |||||||||
Citation | Journal: Biochem. J. / Year: 2009 Title: Structure-activity analysis of aging and reactivation of human butyrylcholinesterase inhibited by analogues of tabun. Authors: Carletti, E. / Aurbek, N. / Gillon, E. / Loiodice, M. / Nicolet, Y. / Fontecilla-Camps, J.C. / Masson, P. / Thiermann, H. / Nachon, F. / Worek, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wsl.cif.gz | 134.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wsl.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wsl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/2wsl ftp://data.pdbj.org/pub/pdb/validation_reports/ws/2wsl | HTTPS FTP |
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-Related structure data
Related structure data | 2widC 2wifC 2wigC 2wijC 2wikC 2wilC 1p0iS C: citing same article (ref.) S: Starting model for refinement |
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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: 59745.574 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: S198 IS PHOSPHORAMIDYLATED / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGS / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P06276, cholinesterase |
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-Sugars , 4 types, 6 molecules
#2: 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 |
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#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 Source method: isolated from a genetically manipulated source |
#5: Sugar |
-Non-polymers , 6 types, 402 molecules
#6: Chemical | ChemComp-CL / |
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#7: Chemical | ChemComp-NA / |
#8: Chemical | ChemComp-SO4 / |
#9: Chemical | ChemComp-EFS / |
#10: Chemical | ChemComp-F / |
#11: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 45 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 483 TO GLN ...ENGINEERED |
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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: 2.8 Å3/Da / Density % sol: 55.7 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES BUFFER PH 6.5, 2.1M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 51418 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 4.35 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P0I Resolution: 2→48.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.254 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.899 Å2
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Refinement step | Cycle: LAST / Resolution: 2→48.87 Å
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Refine LS restraints |
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