Crystal structure of chicken md-1 complexed with lipid iva

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 54% strand (DSSP).

Ligands and binding sites

• LP4 · 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose · ligand · 2 copies · chains A, B
• 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 · 2 copies · chains A, B
• GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 587 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 3MU3 · Crystal structure of chicken MD-1 complexed with lipid IVa · the same entry in another collection · chain A against A, TM-score 1.00
• Q90890 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 86 (Q90890) · a predicted model of the same protein · chain B 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 Q90890
• Elsewhere: RCSB PDB 3MU3 · PDBe 3MU3 · UniProt Q90890