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Yorodumi- PDB-6xyy: Update of ACHE FROM DROSOPHILA MELANOGASTER COMPLEX WITH TACRINE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xyy | |||||||||||||||
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Title | Update of ACHE FROM DROSOPHILA MELANOGASTER COMPLEX WITH TACRINE DERIVATIVE 9-(3-PHENYLMETHYLAMINO)-1,2,3,4-TETRAHYDROACRIDINE | |||||||||||||||
Components | Acetylcholinesterase | |||||||||||||||
Keywords | HYDROLASE / acetylcholinesterase / insect / inhibitor / complex | |||||||||||||||
Function / homology | Function and homology information Aspirin ADME / Neurotransmitter clearance / Synthesis of PC / choline catabolic process / sulfate binding / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase ...Aspirin ADME / Neurotransmitter clearance / Synthesis of PC / choline catabolic process / sulfate binding / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / side of membrane / synaptic cleft / chemical synaptic transmission / synapse / protein homodimerization activity / extracellular space / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||||||||
Authors | Nachon, F. / Sussman, J.L. | |||||||||||||||
Citation | Journal: Molecules / Year: 2020 Title: A Second Look at the Crystal Structures ofDrosophila melanogasterAcetylcholinesterase in Complex with Tacrine Derivatives Provides Insights Concerning Catalytic Intermediates and the Design of ...Title: A Second Look at the Crystal Structures ofDrosophila melanogasterAcetylcholinesterase in Complex with Tacrine Derivatives Provides Insights Concerning Catalytic Intermediates and the Design of Specific Insecticides. Authors: Nachon, F. / Rosenberry, T.L. / Silman, I. / Sussman, J.L. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xyy.cif.gz | 279.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xyy.ent.gz | 189.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xyy_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6xyy_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6xyy_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 6xyy_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/6xyy ftp://data.pdbj.org/pub/pdb/validation_reports/xy/6xyy | HTTPS FTP |
-Related structure data
Related structure data | 6xysC 6xyuC 1qon 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64654.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ace, CG17907 / Plasmid: S2-SEC 1/3 / Cell line (production host): SCHNEIDER LINE 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P07140, acetylcholinesterase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-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 |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 148 molecules
#3: Chemical | ChemComp-PPI / |
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#4: Chemical | ChemComp-760 / |
#6: Chemical | ChemComp-SO4 / |
#7: Chemical | ChemComp-CL / |
#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.86 Å3/Da / Density % sol: 57.03 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 13% MPEG2000, 0.1 M ammonium sulfate, 0.03 M leucine, 0.1 M acetate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å |
Detector | Type: Brandeis B4 / Detector: CCD / Date: Jun 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.78 Å / Num. obs: 20596 / % possible obs: 95.98 % / Redundancy: 5 % / Biso Wilson estimate: 50.19 Å2 / Rrim(I) all: 0.038 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.7→2.796 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1809 / Rrim(I) all: 0.274 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qon 1qon Resolution: 2.7→29.78 Å / SU ML: 0.3542 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9012
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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