Crystal structure of gitr complex with gitr-L

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 43% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, R, S

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

4 interfaces between chains.

• A–B · 402 Ų buried · 5 hydrogen bonds · protein-protein
• A–R · 402 Ų buried · 6 hydrogen bonds · protein-protein
• B–S · 402 Ų buried · 7 hydrogen bonds · protein-protein
• R–S · 304 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

• 7LAW · crystal structure of GITR complex with GITR-L · the same entry in another collection · chain B against B, TM-score 1.00
• Q9UNG2 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 18… · a predicted model of the same protein · chain A against A, TM-score 0.96
• Q9Y5U5 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain R against A, TM-score 0.90

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 Q9UNG2
• Every structure of UniProt Q9Y5U5
• Elsewhere: RCSB PDB 7LAW · PDBe 7LAW · UniProt Q9UNG2 · UniProt Q9Y5U5