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Yorodumi- PDB-2wid: NONAGED FORM OF HUMAN BUTYRYLCHOLINESTERASE INHIBITED BY TABUN AN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wid | |||||||||
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Title | NONAGED FORM OF HUMAN BUTYRYLCHOLINESTERASE INHIBITED BY TABUN ANALOGUE TA1 | |||||||||
Components | CHOLINESTERASE | |||||||||
Keywords | HYDROLASE / AGING / INHIBITION / POLYMORPHISM / 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 / 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: 2.3 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 | 2wid.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wid.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 2wid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/2wid ftp://data.pdbj.org/pub/pdb/validation_reports/wi/2wid | HTTPS FTP |
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-Related structure data
Related structure data | 2wifC 2wigC 2wijC 2wikC 2wilC 2wslC 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: 59713.512 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-557 / 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 , 3 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | |
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-Non-polymers , 5 types, 346 molecules
#4: Chemical | ChemComp-TUN / | ||||
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#5: Chemical | ChemComp-NA / | ||||
#6: Chemical | ChemComp-CL / #7: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 17 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 455 TO GLN ...ENGINEERED |
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Nonpolymer details | ETHYL-N-DIETHYL PHOSPHORAM |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.28 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.1 M AMMONIUM SULFATE, 100 MM MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 27, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.8 Å / Num. obs: 34103 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.35 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 5.3 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P0I Resolution: 2.3→47.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.616 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NULL
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→47.84 Å
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Refine LS restraints |
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