Research workbench
Crystal structure of bak core domain BH3-groove-dimer in complex with E. COLI lipid
Analyse Crystal structure of bak core domain BH3-groove-dimer in complex with E. COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UXM
- Type
- protein
- Length
- 470 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2 homologous ANTAGONIST/KILLER
- UniProt
- Q16611
- Ligands
- PEE
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | BCL-2 homologous ANTAGONIST/KILLER | protein | 79 | 81% helix, 0% strand | Q16611 |
| B, D | BCL-2 homologous ANTAGONIST/KILLER | protein | 77 | 82% helix, 0% strand | Q16611 |
| F | BCL-2 homologous ANTAGONIST/KILLER | protein | 79 | 81% helix, 0% strand | Q16611 |
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.67 | 0.76 | 58 | PEE |
| 2 | 660 | 0.67 | 0.75 | 57 | PEE |
| 3 | 590 | 0.66 | 0.75 | 48 | PEE |
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
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