Primary Citation PubMed: 16193063
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Loop B is a major structural component of the 5-HT3 receptor.
(2008) Biophys J 95
PubMed: 18931259 | PubMedCentral: PMC2599823 | DOI: 10.1529/biophysj.108.135624
( E ) Small antagonist bound, (modeled from AChBP with 2-methyllcaconitine, PDB ID 2byr) ( F ) Overlays of the modeled loop B backbones from A–E compiled with Swiss-PdbViewer “magic fi... ”, using residues Ser-177 to Asn-191 as a reference point.
Three-dimensional models of the extracellular region of the 5-HT 3 receptor were built using MODELER 6v2 ( 22 ) based on the crystal structure of AChBP in different states; unbound (Protein Data Bank (PDB) ID 2byn), agonist bound (carbomylcholine, PDB ID 1uv6 and epibatidine, PDB ID 2byq) and antagonist bound (2-methyllcaconitine, PDB ID 2byr and α -cobratoxin, PDB ID 1yi5).
Publication Year: 2008
A structural and mutagenic blueprint for molecular recognition of strychnine and d-tubocurarine by different cys-loop receptors.
(2011) PLoS Biol 9
PubMed: 21468359 | PubMedCentral: PMC3066128 | DOI: 10.1371/journal.pbio.1001034
Accession Numbers Protein Data Bank accession codes for previously published X-ray crystal structures are: Ac-AChBP in complex with lobeline (2bys), epibatidine (2byq), imidacloprid (3c79), thiaclopri... (3c84), HEPES (2br7), polyethyleneglycol (2byn), DMXBA (2wnj), 4OH-DMXBA (2wn9), cocaine (2pgz), anabaseine (2wnl), in silico compound 31 (2w8f), MLA (2byr), in silico compound 35 (2w8g), sulfates (3gua), α-conotoxin ImI (2c9t and 2byp), α-conotoxin PnIA variant (2br8), α-conotoxin TxIA (2uz6), apo state (2w8e), Y53C-MMTS (2xz5) with acetylcholine, Y53C-MTSET (2xz6).
Publication Year: 2011
Identification of a negative allosteric site on human ?4?2 and ?3?4 neuronal nicotinic acetylcholine receptors.
(2011) PLoS One 6
PubMed: 21949802 | PubMedCentral: PMC3174232 | DOI: 10.1371/journal.pone.0024949
Two roughly aligned AChBP templates (PDB ID: 1UWG and PDB ID: 2BYR) were used with symmetry restraints.
Four different crystallographic templates were used in the homology modeling process: three different molluskan species of AChBP (PDB IDs: 1UW6  , 2BYR  , and 2BJ0  ) as well as the mouse α1 ECD monomer (PDB ID: 2QC1  ).
An integrated catch-and-hold mechanism activates nicotinic acetylcholine receptors.
(2012) J Gen Physiol 140
PubMed: 22732309 | PubMedCentral: PMC3382718 | DOI: 10.1085/jgp.201210801
: 2WN9 , 2WNL , 2BYN (apo-), 2PGZ , 2W8F , 2W8G , 2XYT , 2WNJ , 2BYQ , 2BR7 , 3C79 , 2BYR , 2XYS , 3GUA , 3C84 , 2WNC , 2XZ6 , 2XZ5 , and 2BYS .
Publication Year: 2012
Structural characterization of binding mode of smoking cessation drugs to nicotinic acetylcholine receptors through study of ligand complexes with acetylcholine-binding protein.
(2012) J Biol Chem 287
PubMed: 22553201 | PubMedCentral: PMC3390607 | DOI: 10.1074/jbc.M112.360347
Ribbon representation of LsAChBP in complex with nicotine ( blue ), cytisine ( orange ), varenicline ( green ), methyllycaconitine ( gray , PDB code 2BYR ) and DMXBA ( pink , PDB code 2WNJ ) superpose... with respect to their principal face.
Design, synthesis, and structure-activity relationships of highly potent 5-HT? receptor ligands.
(2012) J Med Chem 55
PubMed: 23006041 | PubMedCentral: PMC3504484 | DOI: 10.1021/jm300801u
10026168 PDB: 2BYR , 2PGZ , 2BYS , 2XYT .
Structural waters located in this binding pocket of the 2WNC crystal structure form a conserved protein–ligand H-bond interaction network in several other AChBP crystals containing small competitive antagonists (e.g., 2BYR , 2PGZ , 2BYS , 2XYT ( 44 )), and were included in the 5-HT 3 A receptor model.
(a) Overlay of the waters participating in the structural water network in several different AChBP crystal structures (red: 2WNC ; blue: 2BYR ; cyan: 2PGZ ; green: 2BYS ; yellow: 2XYT ).
High-Throughput parallel blind Virtual Screening using BINDSURF.
(2012) BMC Bioinformatics 13 Suppl 14
PubMed: 23095663 | PubMedCentral: PMC3504923 | DOI: 10.1186/1471-2105-13-S14-S13
Figure 7 Surface screening results for PDB: 2BYR .
In the case of acetylcholine-binding proteins (PDB: 2BYR ), which provide very useful information for the modeling of the extracellular domain of pentameric ligand-Gated ion channels, we also obtained good agreement with the experimental results, as shown in Figure 7 .
Surface screening results for PDB: 2BYR .
Assembly of a ?-? stack of ligands in the binding site of an acetylcholine-binding protein.
(2013) Nat Commun 4
PubMed: 23695669 | PubMedCentral: PMC3674282 | DOI: 10.1038/ncomms2900
However, MLA (PDB:2BYR) is in a different site closer to the five-fold axis than VUF9432, which uses a lower, more external cavity ( Fig. 2b ).
Publication Year: 2013
Structure-activity relationships of quinoxaline-based 5-HT3A and 5-HT3AB receptor-selective ligands.
(2013) ChemMedChem 8
PubMed: 23640722 | PubMedCentral: PMC4063337 | DOI: 10.1002/cmdc.201300032
Structural waters located in the binding pocket of the original crystal structure (PDB code: 2WNC) 19 form a conserved protein–ligand hydrogen bond interaction network in several other AChBP c... ystals (e.g., 2BYR, 2PGZ, 2BYS, 2XYT) and were included in the 5-HT 3 AB receptor model.
Photo-antagonism of the GABAA receptor.
(2014) Nat Commun 5
PubMed: 25072879 | PubMedCentral: PMC4124873 | DOI: 10.1038/ncomms5454
For antagonists of comparable size to gabazine and GZ-B1, such as methyllycaconitine, the positioning of loop C in AChBP is unchanged (PDB: 2BYR) 36 .
Publication Year: 2014
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