Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 52% strand (DSSP).

Ligands and binding sites

• CD · Cadmium ion · metal · 8 copies · chains L, H
• CL · Chloride ion · ion · 2 copies · chains H

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

3 interfaces between chains.

• L–H · 1673 Ų buried · 13 hydrogen bonds · protein-protein
• H–P · 409 Ų buried · 5 hydrogen bonds · protein-protein
• L–P · 217 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 1SM3 · Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope · the same entry in another collection · chain L against L, TM-score 1.00
• P01801 · AlphaFold monomer V2.0 prediction for ig heavy chain V-III region J606 (P01801) · a predicted model of the same protein · chain H against A, TM-score 0.54
• P01723 · AlphaFold monomer V2.0 prediction for ig lambda-1 chain V region (P01723) · a predicted model of the same protein · chain L against A, TM-score 0.44
• P15941 · AlphaFold monomer V2.0 prediction for mucin-1 (P15941) · a predicted model of the same protein · chain P against A, TM-score 0.33

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 P01723
• Every structure of UniProt P01801
• Every structure of UniProt P15941
• Elsewhere: RCSB PDB 1SM3 · PDBe 1SM3 · UniProt P01723 · UniProt P01801 · UniProt P15941