Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest fragment A1A1A1 of type I collagen

Structure

x-ray diffraction · 5 distinct chains · 33% helix, 0% strand (DSSP).

Ligands and binding sites

• GOL · Glycerol · additive · 5 copies · chains A, B, C, E, F

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

11 interfaces between chains.

• A–C · 1813 Ų buried · 21 hydrogen bonds · protein-protein
• D–F · 1727 Ų buried · 15 hydrogen bonds · protein-protein
• B–C · 1680 Ų buried · 19 hydrogen bonds · protein-protein
• A–B · 1632 Ų buried · 18 hydrogen bonds · protein-protein
• E–F · 1596 Ų buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified, 2 disulfide (engineered, disulfide).

Compared structures

• 5CVB · Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest… · the same entry in another collection · chain A against A, TM-score 1.00
• Q14055 · AlphaFold monomer V2.0 prediction for collagen alpha-2(IX) chain (Q14055) · a predicted model of the same protein · chain E against A, TM-score 0.49
• P20849 · AlphaFold monomer V2.0 prediction for collagen alpha-1(IX) chain (P20849) · a predicted model of the same protein · chain A against A, TM-score 0.45
• Q14050 · AlphaFold monomer V2.0 prediction for collagen alpha-3(IX) chain (Q14050) · a predicted model of the same protein · chain C against A, TM-score 0.44

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 P02452
• Every structure of UniProt P20849
• Every structure of UniProt Q14055
• Every structure of UniProt Q14050
• Elsewhere: RCSB PDB 5CVB · PDBe 5CVB · UniProt P02452 · UniProt P20849 · UniProt Q14055 · UniProt Q14050