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Yorodumi- PDB-7d9q: Crystal Structure of Recombinant Human Acetylcholinesterase in Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d9q | ||||||
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Title | Crystal Structure of Recombinant Human Acetylcholinesterase in Complex with Compound 7 | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / AchE inhibitor / complex structure | ||||||
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 / acetylcholinesterase / amyloid precursor protein metabolic process / 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 / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / Synthesis, secretion, and deacylation of Ghrelin / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / positive regulation of protein secretion / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / nervous system development / amyloid-beta binding / cell adhesion / hydrolase activity / 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 / molecular replacement / Resolution: 2.66 Å | ||||||
Authors | Liu, Q.F. / Yin, W.C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Kinetics-Driven Drug Design Strategy for Next-Generation Acetylcholinesterase Inhibitors to Clinical Candidate. Authors: Zhou, Y. / Fu, Y. / Yin, W. / Li, J. / Wang, W. / Bai, F. / Xu, S. / Gong, Q. / Peng, T. / Hong, Y. / Zhang, D. / Zhang, D. / Liu, Q. / Xu, Y. / Xu, H.E. / Zhang, H. / Jiang, H. / Liu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d9q.cif.gz | 219.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d9q.ent.gz | 172.9 KB | Display | PDB format |
PDBx/mmJSON format | 7d9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d9q_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7d9q_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7d9q_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 7d9q_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/7d9q ftp://data.pdbj.org/pub/pdb/validation_reports/d9/7d9q | HTTPS FTP |
-Related structure data
Related structure data | 7d9oC 7d9pC 4ey7S 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: 60825.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | 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: 4.22 Å3/Da / Density % sol: 70.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.16-0.22M potassium nitrate, 16-20% polyethylene glycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→50 Å / Num. obs: 60606 / % possible obs: 100 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.697 / Rpim(I) all: 0.168 / Rrim(I) all: 0.718 / Χ2: 1 / Net I/σ(I): 3.4 / Num. measured all: 1094103 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ey7 Resolution: 2.66→49.8 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.33 Å2 / Biso mean: 42.6802 Å2 / Biso min: 19.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.66→49.8 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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