Structure of fucosylated D-antimicrobial peptide SB10 in complex with the fucose-binding lectin pa-iil at 1.707 ångström resolution

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 64% strand (DSSP).

Ligands and binding sites

• DLE · D-leucine · ligand · 2 copies · chains A, B, C
• ZDC · 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid · sugar · 2 copies · chains A, B, C
• CA · Calcium ion · metal · 2 copies · chains A
• NH2 · Amino group · ion · 2 copies · chains B, C

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 251 Ų buried · 0 hydrogen bonds · protein-protein
• A–B · 103 Ų buried · 1 hydrogen bond · protein-protein
• A–C · 33 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 d-amino, 2 covalent (D-amino acid, covalent ligand).

Compared structures

• 6Q8H · Structure of Fucosylated D-antimicrobial peptide SB10 in complex with the Fucose-binding… · the same entry in another collection · 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 A0A069Q9V4
• Elsewhere: RCSB PDB 6Q8H · PDBe 6Q8H · UniProt A0A069Q9V4