Crystal structure of EMS16, an antagonist of collagen receptor integrin ALPHA2BETA1 (GPIA/IIA)

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 36% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
• CL · Chloride ion · ion · chains A, B
• GOL · Glycerol · additive · 4 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, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1933 Ų buried · 45 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

• 1UKM · Crystal structure of EMS16, an Antagonist of collagen receptor integrin alpha2beta1… · the same entry in another collection · chain A against A, TM-score 1.00
• Q7T2Q0 · AlphaFold monomer V2.0 prediction for snaclec EMS16 subunit beta (Q7T2Q0) · a predicted model of the same protein · chain B against A, TM-score 0.99
• Q7T2Q1 · AlphaFold monomer V2.0 prediction for snaclec EMS16 subunit alpha (Q7T2Q1) · 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 Q7T2Q1
• Every structure of UniProt Q7T2Q0
• Elsewhere: RCSB PDB 1UKM · PDBe 1UKM · UniProt Q7T2Q1 · UniProt Q7T2Q0