Crystal structure of bak core domain BH3-groove-dimer in complex with popc and C8E4

Structure

x-ray diffraction · 4 distinct chains · 81% helix, 0% strand (DSSP).

Ligands and binding sites

• LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · chains A, B
• SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
• C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 8 copies · chains A, D, B, C
• EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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 · 1949 Ų buried · 20 hydrogen bonds · protein-protein
• C–D · 1911 Ų buried · 22 hydrogen bonds · protein-protein
• B–D · 723 Ų buried · 11 hydrogen bonds · protein-protein
• B–C · 133 Ų buried · 2 hydrogen bonds · protein-protein
• A–D · 127 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 6UXQ · Crystal structure of BAK core domain BH3-groove-dimer in complex with POPC and C8E4 · the same entry in another collection · chain D against D, TM-score 1.00
• Q16611 · AlphaFold monomer V2.0 prediction for BCL-2 homologous ANTAGONIST/KILLER (Q16611) · a predicted model of the same protein · chain C against A, TM-score 0.71

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 Q16611
• Elsewhere: RCSB PDB 6UXQ · PDBe 6UXQ · UniProt Q16611