Crystal structure of leca lectin complexed with a divalent galactoside at 1.65 ångström

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 45% strand (DSSP).

Ligands and binding sites

• CN8 · (4S)-N-ethyl-4-{[N-methyl-3-(1-{2-[(4-sulfanylbenzoyl)amino]ethyl}-1H-1,2,3-triazol-4-yl)-L-alanyl]amino}-L-prolinamide · ligand · 4 copies · chains A, B, C, D
• GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
• CA · Calcium ion · metal · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 2 copies · chains A, D
• 1PE · Pentaethylene glycol · additive · 4 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 2 copies · chains B

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

6 interfaces between chains.

• A–B · 1047 Ų buried · 10 hydrogen bonds · protein-protein
• C–D · 1034 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 381 Ų buried · 9 hydrogen bonds · protein-protein
• A–D · 380 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 247 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (oxidation, nonstandard).

Compared structures

• 4CP9 · Crystal structure OF lecA lectin complexed with a divalent galactoside at 1.65 angstrom · the same entry in another collection · chain A against A, TM-score 1.00
• Q05097 · AlphaFold monomer V2.0 prediction for pa-I galactophilic lectin (Q05097) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q05097
• Elsewhere: RCSB PDB 4CP9 · PDBe 4CP9 · UniProt Q05097