Concanavalin a complexed to a synthetic analog of the trimannoside

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).

Ligands and binding sites

• H1M · methyl 2-deoxy-2-(2-hydroxyethyl)-alpha-D-mannopyranoside · ligand · 4 copies · chains A, B, C, D
• MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
• MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
• CA · Calcium ion · metal · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 4 copies · chains A, D, B, C

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• B–C · 1256 Ų buried · 22 hydrogen bonds · protein-protein
• A–D · 1199 Ų buried · 18 hydrogen bonds · protein-protein

Compared structures

• 3D4K · Concanavalin A Complexed to a Synthetic Analog of the Trimannoside · the same entry in another collection · chain D against D, TM-score 1.00
• P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain A against A, TM-score 0.50

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 P02866
• Elsewhere: RCSB PDB 3D4K · PDBe 3D4K · UniProt P02866