Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 6.5

Structure

x-ray diffraction · resolution 1.95 · 1 distinct chain · 7% helix, 48% strand (DSSP).

Ligands and binding sites

• 6Y2 · ~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-2-[(2~{R},3~{S}, 4~{R},5~{R},6~{S})-5-acetamido-2-(hydroxymethyl)-6-(4-nitrophenoxy)-4-oxidanyl-oxan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C, D, B
• FUC · alpha-L-fucopyranose · sugar · 3 copies
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• BMA · beta-D-mannopyranose · sugar
• XYP · beta-D-xylopyranose · sugar
• CA · Calcium ion · metal · 4 copies · chains A, B, C, D
• MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
• ACT · Acetate ion · additive · 6 copies · chains A, B, C, D

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 · 1193 Ų buried · 18 hydrogen bonds · protein-protein
• C–D · 1186 Ų buried · 18 hydrogen bonds · protein-protein
• A–D · 613 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 607 Ų buried · 6 hydrogen bonds · protein-protein
• A–C · 19 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan (N-glycosylation).

Compared structures

• 5KXD · Wisteria floribunda lectin in complex with GALNAC(BETA1-4)GLCNAC (lacdinac) at pH 6.5 · 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
• Elsewhere: RCSB PDB 5KXD · PDBe 5KXD