Peanut lectin complexed with divalent N-beta-D-galactopyranosyl-L- tartaramidoyl derivative (dingt)

Structure

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

Ligands and binding sites

• QSG · (2R,3R)-N-[(1-{(3S,3aR,6S,6aR)-6-[4-({[(2R,3R)-2,3-dihydroxy-4-oxo-4-{[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]amino}butanoyl]amino}methyl)-1H-1,2,3-triazol-1-yl]hexahydrofuro[3,2-b]furan-3-yl}-1H-1,2,3-triazol-4-yl)methyl]-2,3-dihydroxy-N'-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]butanediamide (non-preferred name) · ligand · 4 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

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.

• A–D · 991 Ų buried · 12 hydrogen bonds · protein-protein
• B–C · 984 Ų buried · 11 hydrogen bonds · protein-protein
• A–B · 678 Ų buried · 3 hydrogen bonds · protein-protein
• C–D · 623 Ų buried · 11 hydrogen bonds · protein-protein
• B–D · 64 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 6V95 · Peanut lectin complexed with divalent N-beta-D-galactopyranosyl-L-tartaramidoyl… · 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 6V95 · PDBe 6V95 · UniProt P02872