Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest fragment A1A2A1 of type I collagen

Structure

x-ray diffraction · 6 distinct chains · 37% helix, 1% strand (DSSP).

Ligands and binding sites

• GOL · Glycerol · additive · 2 copies · chains A, B, D, 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

10 interfaces between chains.

• A–C · 1759 Ų buried · 17 hydrogen bonds · protein-protein
• A–B · 1626 Ų buried · 19 hydrogen bonds · protein-protein
• B–C · 1604 Ų buried · 21 hydrogen bonds · protein-protein
• D–F · 1475 Ų buried · 15 hydrogen bonds · protein-protein
• E–F · 1325 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 2 disulfide (engineered, disulfide).

Compared structures

• 5CVA · Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest… · the same entry in another collection · chain D against D, TM-score 1.00
• Q14050 · AlphaFold monomer V2.0 prediction for collagen alpha-3(IX) chain (Q14050) · a predicted model of the same protein · chain F against A, TM-score 0.52
• 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 0.47
• 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
• P08123 · AlphaFold monomer V2.0 prediction for collagen alpha-2(I) chain (P08123) · a predicted model of the same protein · chain D against A, TM-score 0.43

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 P08123
• Every structure of UniProt P20849
• Every structure of UniProt P02452
• Every structure of UniProt Q14055
• Every structure of UniProt Q14050
• Elsewhere: RCSB PDB 5CVA · PDBe 5CVA · UniProt P08123 · UniProt P20849 · UniProt P02452 · UniProt Q14055 · UniProt Q14050