Open AccessUnexpected features in the Protein Data Bank entries 3qd1 and 4i8e: the structural description of the binding of the serine‐rich repeat adhesin GspB to host cell carbohydrate receptor is not a solved issue
Author(s) -
Muller Yves A.
Publication year - 2013
Publication title -
acta crystallographica section f
Language(s) - English
Resource type - Journals
ISSN - 1744-3091
DOI - 10.1107/s1744309113014383
Subject(s) - bacterial adhesin , protein data bank (rcsb pdb) , disaccharide , protein data bank , van der waals force , chemistry , docking (animal) , crystallography , receptor , carbohydrate , serine , molecule , stereochemistry , protein structure , biochemistry , gene , phosphorylation , medicine , nursing , organic chemistry , escherichia coli
The structure of a complex between a fragment of the adhesin GspB from Streptococcus gordonii and a disaccharide (PDB entries 3qd1 and 4i8e ) has recently been proposed to identify the binding site for the sialyl‐T antigen recognized by GspB. This structure exhibits numerous unrealistic and unusual features such as an excessive number of van der Waals clashes and a lack of correlation between atomic structure and experimental electron density. Here, it is shown that the crystallographic data can be fully explained by an alternative model, namely replacing the disaccharide with a buffer molecule. The conclusion is that the experimental data are likely to contain no information regarding the carbohydrate receptor binding site in GspB or the interaction of GspB with host cell receptors.