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Yorodumi- PDB-5nuu: Torpedo californica acetylcholinesterase in complex with a chloro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nuu | |||||||||
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Title | Torpedo californica acetylcholinesterase in complex with a chlorotacrine-tryptophan hybrid inhibitor | |||||||||
Components | Acetylcholinesterase | |||||||||
Keywords | HYDROLASE / Alzheimer's disease / Tacrine / Acetylcholinesterase / Acetylcholiensterase inhibitor | |||||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / plasma membrane Similarity search - Function | |||||||||
Biological species | Tetronarce californica (Pacific electric ray) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Caliandro, R. / Pesaresi, A. / Lamba, D. | |||||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2019 Title: Novel tacrine-tryptophan hybrids: Multi-target directed ligands as potential treatment for Alzheimer's disease. Authors: Chalupova, K. / Korabecny, J. / Bartolini, M. / Monti, B. / Lamba, D. / Caliandro, R. / Pesaresi, A. / Brazzolotto, X. / Gastellier, A.J. / Nachon, F. / Pejchal, J. / Jarosova, M. / ...Authors: Chalupova, K. / Korabecny, J. / Bartolini, M. / Monti, B. / Lamba, D. / Caliandro, R. / Pesaresi, A. / Brazzolotto, X. / Gastellier, A.J. / Nachon, F. / Pejchal, J. / Jarosova, M. / Hepnarova, V. / Jun, D. / Hrabinova, M. / Dolezal, R. / Zdarova Karasova, J. / Mzik, M. / Kristofikova, Z. / Misik, J. / Muckova, L. / Jost, P. / Soukup, O. / Benkova, M. / Setnicka, V. / Habartova, L. / Chvojkova, M. / Kleteckova, L. / Vales, K. / Mezeiova, E. / Uliassi, E. / Valis, M. / Nepovimova, E. / Bolognesi, M.L. / Kuca, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nuu.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nuu.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nuu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/5nuu ftp://data.pdbj.org/pub/pdb/validation_reports/nu/5nuu | HTTPS FTP |
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-Related structure data
Related structure data | 6i0bC 6i0cC 5e4tS 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
#1: Protein | Mass: 61325.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetronarce californica (Pacific electric ray) References: UniProt: P04058, acetylcholinesterase | ||||
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#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-9A5 / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.65 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: MES 100 mM, pH 6.2 PEG200 30% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.49 Å / Num. obs: 35012 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.224 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 9.8 % / Rmerge(I) obs: 2.572 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E4T Resolution: 2.5→48.49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.617 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.232 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.49 Å
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Refine LS restraints |
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