Design of a short thermally stable alpha-helix embedded in a macrocycle

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).

Ligands and binding sites

• H00 · 4-sulfanylbutanoic acid · ligand · 6 copies · chains A, B, C, E, F, D
• B0I · 3,3'-dimethyl-1,1'-biphenyl · ligand · 6 copies · chains A, B, F, C, E, D
• NH2 · Amino group · ion · 6 copies · chains A, B, E, F, D, C

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

7 interfaces between chains.

• B–C · 184 Ų buried · 4 hydrogen bonds · protein-protein
• A–F · 178 Ų buried · 4 hydrogen bonds · protein-protein
• E–D · 177 Ų buried · 3 hydrogen bonds · protein-protein
• A–B · 151 Ų buried · 0 hydrogen bonds · protein-protein
• D–C · 106 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 covalent, 6 d-amino (covalent ligand, D-amino acid).

Compared structures

• 6B17 · Design of a short thermally stable alpha-helix embedded in a macrocycle · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Elsewhere: RCSB PDB 6B17 · PDBe 6B17