5A70
Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with lewis x tetrasaccharide
Summary for 5A70
Entry DOI | 10.2210/pdb5a70/pdb |
Related | 5A6Q 5A6X 5A6Y 5A6Z |
Descriptor | LECB, alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose, CALCIUM ION, ... (5 entities in total) |
Functional Keywords | sugar binding protein, lectin, lecb lewis x antigen |
Biological source | PSEUDOMONAS AERUGINOSA |
Total number of polymer chains | 4 |
Total formula weight | 49986.11 |
Authors | Sommer, R.,Wagner, S.,Varrot, A.,Khaledi, A.,Haussler, S.,Imberty, A.,Titz, A. (deposition date: 2015-07-02, release date: 2016-07-27, Last modification date: 2024-01-10) |
Primary citation | Lepsik, M.,Sommer, R.,Kuhaudomlarp, S.,Lelimousin, M.,Paci, E.,Varrot, A.,Titz, A.,Imberty, A. Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study. Eur.J.Med.Chem., 177:212-220, 2019 Cited by PubMed Abstract: Pathogenic micro-organisms utilize protein receptors (lectins) in adhesion to host tissues, a process that in some cases relies on the interaction between lectins and human glycoconjugates. Oligosaccharide epitopes are recognized through their three-dimensional structure and their flexibility is a key issue in specificity. In this paper, we analysed by X-ray crystallography the structures of the LecB lectin from two strains of Pseudomonas aeruginosa in complex with Lewis x oligosaccharide present on cell surfaces of human tissues. An unusual conformation of the glycan was observed in all binding sites with a non-canonical syn orientation of the N-acetyl group of N-acetyl-glucosamine. A PDB-wide search revealed that such an orientation occurs only in 4% of protein/carbohydrate complexes. Theoretical chemistry calculations showed that the observed conformation is unstable in solution but stabilised by the lectin. A reliable description of LecB/Lewis x complex by force field-based methods had proven especially challenging due to the special feature of the binding site, two closely apposed Ca ions which induce strong charge delocalisation. By comparing various force-field parametrisations, we propose a general strategy which will be useful in near future for designing carbohydrate-based ligands (glycodrugs) against other calcium-dependent protein receptors. PubMed: 31146126DOI: 10.1016/j.ejmech.2019.05.049 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (1.6 Å) |
Structure validation
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