E-selectin lectin, EGF-like and two scr domains complexed with glycomimetic ligand NV355

Structure

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

Ligands and binding sites

• C5K · (2~{S})-3-cyclohexyl-2-[(2~{R},3~{S},4~{S},5~{R}, 6~{R})-2-(hydroxymethyl)-6-[(1~{R},2~{R},3~{S})-3-methyl-2-[(2~{R},3~{S},4~{R},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(trifluoromethyl)oxan-2-yl]oxy-cyclohexyl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-propanoic acid · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
• CA · Calcium ion · metal · 2 copies · chains A

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

Modifications

Observed in the structure: 11 disulfide, 7 glycan (disulfide, N-glycosylation).

Compared structures

• 6EYK · E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic ligand NV355 · 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 0.79

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 6EYK · PDBe 6EYK · UniProt P16581