6V7L
The structure of the P212121 crystal form of canavalin at 173 K
Summary for 6V7L
| Entry DOI | 10.2210/pdb6v7l/pdb |
| Descriptor | Canavalin, BENZOIC ACID (3 entities in total) |
| Functional Keywords | precanavalin, proteolytic cleavage, plant protein, vicillim, storage protein, benzoic acid |
| Biological source | Canavalia ensiformis (Jack bean) |
| Total number of polymer chains | 3 |
| Total formula weight | 151516.77 |
| Authors | McPherson, A. (deposition date: 2019-12-08, release date: 2020-02-19, Last modification date: 2023-10-11) |
| Primary citation | McPherson, A. Binding of benzoic acid and anions within the cupin domains of the vicilin protein canavalin from jack bean (Canavalia ensiformis): Crystal structures. Biochem.Biophys.Res.Commun., 524:268-271, 2020 Cited by PubMed Abstract: X-ray intensities extending to 1.4 Å resolution were collected on the P6 hexagonal crystal form of canavalin, and extended to 1.9 Å for the orthorhombic C222 crystals. Structure determination of a new crystal form of canavalin having space group P222 is reported as well. Both the N and C terminal cupin domains contained identifiable ligands. For hexagonal crystals, in the cavity of the C terminal cupin, a molecule of benzoic acid was found, bound through carboxyl oxygens to Histidine 297, asparagine 284 and Arginine 376. The benzene ring was immersed in a cluster of at least 8 hydrophobic amino acid side chains. The N terminal cupin contained a molecule of citrate. Benzoic acid was also found to be present in the C terminal cupins of in the C222 and P222 crystal forms. In rhombohedral crystals, the C terminal cupin domain appeared to be occupied by a phosphate ion, but this was ambiguous. In cubic crystals, both domains were vacant. The N terminal cupin domains of canavalin in the P222 and rhombohedral crystals were also vacant, but the N terminal cupin domain of the C222 crystals contained a ligand whose identity is uncertain, but which has been modeled as HEPES buffer. A possible physiological role for the ligands and their complexes with canavalin is considered. PubMed: 31983433DOI: 10.1016/j.bbrc.2020.01.101 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.8 Å) |
Structure validation
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