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Yorodumi- PDB-4ey6: Crystal Structure of Recombinant Human Acetylcholinesterase in Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ey6 | |||||||||
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Title | Crystal Structure of Recombinant Human Acetylcholinesterase in Complex with (-)-galantamine | |||||||||
Components | Acetylcholinesterase | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / acetylcholinesterase / hydrolase / galantamine / inhibitor / galanthamine / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / choline metabolic process / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3983 Å | |||||||||
Authors | Cheung, J. / Rudolph, M. / Burshteyn, F. / Cassidy, M. / Gary, E. / Love, J. / Height, J. / Franklin, M. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Structures of human acetylcholinesterase in complex with pharmacologically important ligands. Authors: Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M.S. / Gary, E.N. / Love, J. / Franklin, M.C. / Height, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ey6.cif.gz | 232.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ey6.ent.gz | 184.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ey6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ey6_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4ey6_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4ey6_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 4ey6_validation.cif.gz | 60.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/4ey6 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/4ey6 | HTTPS FTP |
-Related structure data
Related structure data | 4ey4C 4ey5C 4ey7SC 4ey8C 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, 2 molecules AB
#1: Protein | Mass: 59447.105 Da / Num. of mol.: 2 / Fragment: UNP Residues 33-574 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
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-Non-polymers , 5 types, 393 molecules
#3: Chemical | #4: Chemical | #6: Chemical | #7: Chemical | ChemComp-PE8 / | #8: Water | ChemComp-HOH / | |
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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: 4.33 Å3/Da / Density % sol: 71.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12 to 18% PEG 3350, 0.2M potassium nitrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.398→50 Å / Num. all: 82061 / Num. obs: 81569 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4EY7 Resolution: 2.3983→47.191 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.25 / σ(F): 0 / Phase error: 21.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3983→47.191 Å
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Refine LS restraints |
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LS refinement shell |
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