5T7P image
Deposition Date 2016-09-05
Release Date 2017-08-09
Last Version Date 2023-10-04
Entry Detail
PDB ID:
5T7P
Title:
Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man
Biological Source:
Source Organism:
Pisum sativum (Taxon ID: 3888)
Method Details:
Experimental Method:
Resolution:
2.16 Å
R-Value Free:
0.22
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Lectin
Gene (Uniprot):LECA
Chain IDs:A, B
Chain Length:236
Number of Molecules:2
Biological Source:Pisum sativum
Primary Citation
Crystal structure of Pisum arvense seed lectin (PAL) and characterization of its interaction with carbohydrates by molecular docking and dynamics.
Arch. Biochem. Biophys. 630 27 37 (2017)
PMID: 28754321 DOI: 10.1016/j.abb.2017.07.013

Abstact

The Pisum arvense lectin (PAL), a legume protein belonging to the Vicieae tribe, is capable of specific recognition of mannose, glucose and its derivatives without altering its structure. In this work, the three-dimensional structure of PAL was determined by X-ray crystallography and studied in detail by a combination of molecular docking and molecular dynamics (MD). Crystals belonging to monoclinic space group P21 were grown by the vapor diffusion method at 293 K. The structure was solved at 2.16 Å and was similar to that of other Vicieae lectins. The structure presented Rfactor and Rfree of 17.04% and 22.08%, respectively, with all acceptable geometric parameters. Molecular docking was performed to analyze interactions of the lectin with monosaccharides, disaccharides and high-mannose N-glycans. PAL demonstrated different affinities on carbohydrates, depending on bond orientation and glycosidic linkage present in ligands. Furthermore, the lectin interacted with representative N-glycans in a manner consistent with the biological effects described for Vicieae lectins. Carbohydrate-recognition domain (CRD) in-depth analysis was performed by MD, describing the behavior of CRD residues in complex with ligand, stability, flexibility of the protein over time, CRD volume and topology. This is a first report of its kind for a lectin of the Vicieae tribe.

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