+Open data
-Basic information
Entry | Database: PDB / ID: 5e4t | ||||||||||||
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Title | Acetylcholinesterase Methylene Blue with 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 / MOLECULAR REPLACEMENT / Resolution: 2.43 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 | 5e4t.cif.gz | 233.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e4t.ent.gz | 188.2 KB | Display | PDB format |
PDBx/mmJSON format | 5e4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e4t_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5e4t_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5e4t_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5e4t_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/5e4t ftp://data.pdbj.org/pub/pdb/validation_reports/e4/5e4t | HTTPS FTP |
-Related structure data
Related structure data | 5dlpC 5e2iC 5e4jC 2w9i 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
-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-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 |
#4: 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 |
-Non-polymers , 5 types, 192 molecules
#5: Chemical | ChemComp-MBT / | ||||||
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#6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-PGE / #8: Chemical | ChemComp-EDO / #9: 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 / pH: 6.5 / Details: 46% PEG200 (v/v) in 100 mM NaCl/1 mM MES, pH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→96.23 Å / Num. obs: 35368 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 34.8 |
Reflection shell | Resolution: 2.43→2.52 Å / Redundancy: 2 % / Mean I/σ(I) obs: 5.5 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W9I 2w9i Resolution: 2.43→96.23 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 10.878 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.188 / 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: 47.596 Å2
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Refinement step | Cycle: LAST / Resolution: 2.43→96.23 Å
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