Crystal structure of human desmocollin-2 ectodomain fragment EC2-5

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 42% strand (DSSP).

Ligands and binding sites

• MAN · alpha-D-mannopyranose · sugar · 11 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 3 copies
• CA · Calcium ion · metal · 21 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 5 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, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 215 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 glycan, 6 disulfide (O-glycosylation, disulfide, N-glycosylation, glycation, glycosylation).

Compared structures

• 5ERP · Crystal structure of human Desmocollin-2 ectodomain fragment EC2-5 · the same entry in another collection · chain A against A, TM-score 1.00
• Q02487 · AlphaFold monomer V2.0 prediction for desmocollin-2 (Q02487) · a predicted model of the same protein · chain A against A, TM-score 0.88

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 Q02487
• Elsewhere: RCSB PDB 5ERP · PDBe 5ERP · UniProt Q02487