Crystal structure of the human fyn SH3 domain in complex with a peptide from the hepatitis C virus NS5A-protein

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 41% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · chains E
• ZN · Zinc ion · metal · 2 copies · chains C, D
• NA · Sodium ion · metal · chains A, B
• CL · Chloride ion · ion · chains A
• FMT · Formic acid · additive · 2 copies · chains C, D
• GOL · Glycerol · additive · chains A

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

Pockets

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

Interfaces

8 interfaces between chains.

• A–B · 595 Ų buried · 10 hydrogen bonds · protein-protein
• D–F · 469 Ų buried · 6 hydrogen bonds · protein-protein
• B–D · 418 Ų buried · 8 hydrogen bonds · protein-protein
• A–C · 418 Ų buried · 8 hydrogen bonds · protein-protein
• A–E · 332 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 3UA7 · Crystal Structure of the Human Fyn SH3 domain in complex with a peptide from the… · the same entry in another collection · chain F against F, TM-score 1.00
• P06241 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase fyn (P06241) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P06241
• Every structure of UniProt Q9YKI6
• Elsewhere: RCSB PDB 3UA7 · PDBe 3UA7 · UniProt P06241 · UniProt Q9YKI6