Peanut lectin complexed with divalent N-beta-D-galactopyranosyl-L- succinamoyl derivative (dings)

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).

Ligands and binding sites

• QTY · N-[[1-[(3s,3ar,6s,6ar)-6-[4-[[[4-[[(2R,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]amino]-4-oxidanylidene-butanoyl]amino]methyl]-1,2,3-triazol-1-yl]-2,3,3A,5,6,6A-hexahydrofuro[3,2-b]furan-3-yl]-1, 2,3-triazol-4-yl]methyl]-N'-[(2R,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]butanediamide · ligand · 4 copies · chains A, B, C, D
• MN · Manganese (II) ion · metal · 3 copies · chains A, B, D
• CA · Calcium ion · metal · 3 copies · chains A, B, D

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

Pockets

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

Interfaces

6 interfaces between chains.

• B–C · 984 Ų buried · 12 hydrogen bonds · protein-protein
• A–D · 983 Ų buried · 12 hydrogen bonds · protein-protein
• A–B · 679 Ų buried · 4 hydrogen bonds · protein-protein
• C–D · 594 Ų buried · 11 hydrogen bonds · protein-protein
• B–D · 69 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 6VAV · Peanut lectin complexed with divalent N-beta-D-galactopyranosyl-L-succinamoyl derivative… · the same entry in another collection · chain A against A, TM-score 1.00
• P02872 · AlphaFold monomer V2.0 prediction for galactose-binding lectin (P02872) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P02872
• Elsewhere: RCSB PDB 6VAV · PDBe 6VAV · UniProt P02872