Crystal structure of pd-L1 from P. dioica in complex with adenine

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).

Ligands and binding sites

• ADE · Adenine · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B

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.

Interfaces

1 interface between chains.

• A–B · 334 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 3LE7 · Crystal structure of PD-L1 from P. dioica in complex with adenine · the same entry in another collection · chain A against A, TM-score 1.00
• P84853 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein pd-L1/PD-L2 (P84853) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P84853
• Elsewhere: RCSB PDB 3LE7 · PDBe 3LE7 · UniProt P84853