Crystal structure of the DDR2 discoidin domain bound to a triple-helical collagen peptide

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 31% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · 2 copies · chains B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• B–C · 939 Ų buried · 11 hydrogen bonds · protein-protein
• C–D · 858 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 856 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 376 Ų buried · 2 hydrogen bonds · protein-protein
• A–B · 287 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified, 2 covalent, 2 disulfide (hydroxylation, nonstandard, covalent ligand, disulfide).

Compared structures

• 2WUH · Crystal structure of the DDR2 discoidin domain bound to a triple- helical collagen peptide · the same entry in another collection · chain A against A, TM-score 1.00
• Q16832 · AlphaFold monomer V2.0 prediction for discoidin domain-containing receptor 2 (Q16832) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q16832
• Elsewhere: RCSB PDB 2WUH · PDBe 2WUH · UniProt Q16832