Crystal structure of human md-2 in complex with lipid iva

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 50% strand (DSSP).

Ligands and binding sites

• LP5 · (R)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanamido)-6-(phosphonooxy) tetrahydro-2H-pyran-4-yl) 3-hydroxytetradecanoate · ligand · chains A
• LP4 · 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A

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

Pockets

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

Modifications

Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 2E59 · Crystal structure of human MD-2 in complex with lipid IVa · the same entry in another collection · chain A against A, TM-score 1.00
• Q9Y6Y9 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 96 (Q9Y6Y9) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q9Y6Y9
• Elsewhere: RCSB PDB 2E59 · PDBe 2E59 · UniProt Q9Y6Y9