Crystal structure of bak core domain BH3-groove-dimer in complex with E. COLI lipid

Structure

x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).

Ligands and binding sites

• PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 6 copies · chains A, B, F, C, D, E

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

12 interfaces between chains.

• A–B · 1923 Ų buried · 13 hydrogen bonds · protein-protein
• E–F · 1881 Ų buried · 15 hydrogen bonds · protein-protein
• C–D · 1838 Ų buried · 17 hydrogen bonds · protein-protein
• A–F · 372 Ų buried · 1 hydrogen bond · protein-protein
• B–C · 363 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 6UXM · Crystal structure of BAK core domain BH3-groove-dimer in complex with E. coli lipid · the same entry in another collection · chain F against F, 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 B against A, TM-score 0.69

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 6UXM · PDBe 6UXM · UniProt Q16611