X-ray structure of lfa-1 I-domain in complex with LFA878 at 2.1A resolution

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 25% strand (DSSP).

Ligands and binding sites

• AB8 · (1s,3r,8as)-8-(2-{(4S,6S)-3-(4-hydroxy-3-methoxybenzyl)-4-[2-(methylamino)-2-oxoethyl]-2-oxo-1,3-oxazinan-6-yl}ethyl)-3 ,7-dimethyl-1,2,3,7,8,8A-hexahydronaphthalen-1-yl (2R)-2-methylbutanoate · ligand · 2 copies · chains A, B
• MG · Magnesium 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, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 918 Ų buried · 20 hydrogen bonds · protein-protein

Compared structures

• 1XDG · X-ray structure of LFA-1 I-domain in complex with LFA878 at 2.1A resolution · the same entry in another collection · chain A against A, TM-score 1.00
• P20701 · AlphaFold monomer V2.0 prediction for integrin alpha-L (P20701) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P20701
• Elsewhere: RCSB PDB 1XDG · PDBe 1XDG · UniProt P20701