Bak BH3-in-groove dimer (GFP)

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 38% strand (DSSP).

Ligands and binding sites

• CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains B, D, C, A
• CAC · Cacodylate ion · additive · 6 copies · chains B, D, A, C
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains D, C, A, B

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• D–A · 2303 Ų buried · 25 hydrogen bonds · protein-protein
• B–C · 2285 Ų buried · 21 hydrogen bonds · protein-protein
• D–C · 1016 Ų buried · 9 hydrogen bonds · protein-protein
• B–A · 990 Ų buried · 8 hydrogen bonds · protein-protein
• C–A · 485 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (chromophore).

Compared structures

• 4U2V · Bak BH3-in-Groove dimer (GFP) · the same entry in another collection · chain B against B, TM-score 1.00
• P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain D against A, TM-score 0.75
• 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 0.27

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 P42212
• Every structure of UniProt Q16611
• Elsewhere: RCSB PDB 4U2V · PDBe 4U2V · UniProt P42212 · UniProt Q16611