+Open data
-Basic information
Entry | Database: PDB / ID: 5dlp | ||||||||||||
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Title | Acetylcholinesterase Methylene Blue no PEG | ||||||||||||
Components | Acetylcholinesterase | ||||||||||||
Keywords | HYDROLASE / Inhibitor | ||||||||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / choline metabolic process / acetylcholinesterase activity / side of membrane / synaptic cleft / synapse / extracellular space / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Torpedo californica (Pacific electric ray) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||||||||
Authors | Dym, O. | ||||||||||||
Citation | Journal: Protein Sci. / Year: 2016 Title: The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex. Authors: Dym, O. / Song, W. / Felder, C. / Roth, E. / Shnyrov, V. / Ashani, Y. / Xu, Y. / Joosten, R.P. / Weiner, L. / Sussman, J.L. / Silman, I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dlp.cif.gz | 225.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dlp.ent.gz | 181.4 KB | Display | PDB format |
PDBx/mmJSON format | 5dlp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dlp_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5dlp_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5dlp_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 5dlp_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/5dlp ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dlp | HTTPS FTP |
-Related structure data
Related structure data | 5e2iC 5e4jC 5e4tC 2w9i 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61325.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Torpedo californica (Pacific electric ray) References: UniProt: P04058, acetylcholinesterase |
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-Sugars , 3 types, 3 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 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 31 molecules
#4: Chemical | ChemComp-MBT / | ||
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#6: Chemical | ChemComp-SO4 / #7: 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: 3.98 Å3/Da / Density % sol: 69.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 46% PEG200 (v/v) in 100 mM NaCl/1 mM MES, pH 6.5 / PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→96.18 Å / Num. obs: 27016 / % possible obs: 98.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.7→2.85 Å / Rmerge(I) obs: 0.643 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W9I 2w9i Resolution: 2.7→96.18 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 22.738 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.255 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.018 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→96.18 Å
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Refine LS restraints |
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