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Yorodumi- PDB-6ntl: Crystal Structure of Recombinant Human Acetylcholinesterase Inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ntl | |||||||||
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Title | Crystal Structure of Recombinant Human Acetylcholinesterase Inhibited by A-234 | |||||||||
Components | Acetylcholinesterase | |||||||||
Keywords | hydrolase/hydrolase inhibitor / hydrolase / inhibitor / 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: 2.25 Å | |||||||||
Authors | Bester, S.M. / Guelta, M.A. / Height, J.J. / Pegan, S.D. | |||||||||
Citation | Journal: To Be Published Title: Insights into inhibition of human acetylcholinesterase by Novichok, A-series Nerve Agents Authors: Height, J.J. / Bester, S.M. / Guelta, M.A. / Bae, S.Y. / Cheung, J. / Pegan, S.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ntl.cif.gz | 450.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ntl.ent.gz | 368.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ntl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ntl_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6ntl_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6ntl_validation.xml.gz | 48.7 KB | Display | |
Data in CIF | 6ntl_validation.cif.gz | 73.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/6ntl ftp://data.pdbj.org/pub/pdb/validation_reports/nt/6ntl | HTTPS FTP |
-Related structure data
Related structure data | 6ntgC 6nthC 6ntkC 6ntmC 6ntnC 6ntoC 4ey4S 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
#1: Protein | Mass: 59447.105 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 | ChemComp-7PE / | #4: Chemical | #5: 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: 71.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15-21% polyethylene glycol 3350 (PEG) and 0.17- 0.21M potassium nitrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 99121 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.045 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4885 / CC1/2: 0.846 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EY4 Resolution: 2.25→46.41 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.1 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→46.41 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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