Crystal structure of scfv-SM3 in complex with compound 3

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 52% strand (DSSP).

Ligands and binding sites

• EEN · 2-deoxy-2-[(difluoroacetyl)amino]-alpha-D-galactopyranose · ligand · chains H, P
• EDO · 1,2-ethanediol · additive · 10 copies · chains H, P

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

1 interface between chains.

• H–P · 408 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

• 6FZQ · Crystal structure of scFv-SM3 in complex with compound 3 · the same entry in another collection · chain H against H, TM-score 1.00
• P15941 · AlphaFold monomer V2.0 prediction for mucin-1 (P15941) · a predicted model of the same protein · chain P against A, TM-score 0.48

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 P15941
• Elsewhere: RCSB PDB 6FZQ · PDBe 6FZQ · UniProt P15941