E-selectin lectin, EGF-like and two scr domains complexed with glycomimetic ligand NV354

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 35% strand (DSSP).

Ligands and binding sites

• C5H · (2~{S})-3-cyclohexyl-2-[(2~{R},3~{S},4~{S},5~{R}, 6~{R})-2-(hydroxymethyl)-3,5-bis(oxidanyl)-6-[(1~{R}, 2~{R})-2-[(2~{R},3~{S},4~{R},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(trifluoromethyl)oxan-2-yl]oxycyclohexyl]oxy-oxan-4-yl]oxy-propanoic acid · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
• CA · Calcium ion · metal · 2 copies · chains A, 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, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 378 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 14 glycan (disulfide, N-glycosylation).

Compared structures

• 6EYJ · E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic ligand NV354 · the same entry in another collection · chain A against A, TM-score 1.00
• P16581 · AlphaFold monomer V2.0 prediction for E-selectin (P16581) · a predicted model of the same protein · chain A against A, TM-score 0.78

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 P16581
• Elsewhere: RCSB PDB 6EYJ · PDBe 6EYJ · UniProt P16581