Canavalia maritima lectin complexed with synthetic selenoamino acid

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 45% strand (DSSP).

Ligands and binding sites

• 4WM · (4R)-4-{[(S)-tert-butoxy(hydroxy)methyl]amino}-5-[(1S)-cyclohex-2-en-1-ylselanyl]pentane-1,1-diol · ligand · 2 copies · chains A, B
• CA · Calcium ion · metal · 2 copies · chains A, B
• MN · Manganese (II) ion · metal · 2 copies · chains A, B
• CD · Cadmium ion · metal · chains A
• EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1128 Ų buried · 12 hydrogen bonds · protein-protein

Compared structures

• 5BYN · Canavalia maritima lectin complexed with synthetic selenoamino acid · the same entry in another collection · chain A against A, TM-score 1.00
• P81460 · AlphaFold monomer V2.0 prediction for concanavalin-a (P81460) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P81460
• Elsewhere: RCSB PDB 5BYN · PDBe 5BYN · UniProt P81460