Complex of a low affinity collagen site with the fibronectin 8-9FNI domain pair

Structure

x-ray diffraction · 4 distinct chains · 0% helix, 57% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, E, A
• GOL · Glycerol · additive · chains A

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

4 interfaces between chains.

• A–E · 692 Ų buried · 16 hydrogen bonds · protein-protein
• B–F · 559 Ų buried · 11 hydrogen bonds · protein-protein
• B–E · 414 Ų buried · 7 hydrogen bonds · protein-protein
• B–A · 176 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, hydroxylation, nonstandard).

Compared structures

• 3GXE · Complex of a Low Affinity Collagen Site with the Fibronectin 8-9FnI Domain Pair · the same entry in another collection · chain E against E, TM-score 1.00
• P02751 · AlphaFold monomer V2.0 prediction for fibronectin (P02751) · a predicted model of the same protein · chain B against A, TM-score 0.70
• P02452 · AlphaFold monomer V2.0 prediction for collagen alpha-1(I) chain (P02452) · a predicted model of the same protein · chain E against A, TM-score 0.37

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 P02751
• Every structure of UniProt P02452
• Elsewhere: RCSB PDB 3GXE · PDBe 3GXE · UniProt P02751 · UniProt P02452