Crystal structure of the second and third fibronectin F1 modules in complex with a fragment of staphylococcus aureus fnbpa-5

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 60% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · 2 copies · chains B, C, D
• NH2 · Amino group · ion · chains 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, 1 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 1029 Ų buried · 35 hydrogen bonds · protein-protein
• C–D · 1013 Ų buried · 29 hydrogen bonds · protein-protein
• A–D · 249 Ų buried · 0 hydrogen bonds · protein-protein
• B–C · 229 Ų buried · 0 hydrogen bonds · protein-protein
• A–C · 217 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

• 3CAL · Crystal structure of the second and third fibronectin F1 modules in complex with a… · the same entry in another collection · chain D against D, TM-score 1.00
• P02751 · AlphaFold monomer V2.0 prediction for fibronectin (P02751) · a predicted model of the same protein · chain C against A, TM-score 0.83
• P14738 · AlphaFold monomer V2.0 prediction for fibronectin-binding protein a (P14738) · a predicted model of the same protein · chain B against A, TM-score 0.27

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 P14738
• Elsewhere: RCSB PDB 3CAL · PDBe 3CAL · UniProt P02751 · UniProt P14738