Research workbench
Bak core latch dimer in complex with bim-rt - tetragonal
Analyse Bak core latch dimer in complex with bim-rt - tetragonal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VWW
- Type
- protein
- Length
- 333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2 homologous ANTAGONIST/KILLER; BCL-2-like protein 11
- UniProt
- Q16611, O43521
- Ligands
- BR
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 82% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2 homologous ANTAGONIST/KILLER | protein | 147 | 81% helix, 0% strand | Q16611 |
| B | BCL-2 homologous ANTAGONIST/KILLER | protein | 142 | 82% helix, 1% strand | Q16611 |
| C | BCL-2-like protein 11 | protein | 25 | 80% helix, 4% strand | O43521 |
| D | BCL-2-like protein 11 | protein | 19 | 89% helix, 0% strand | O43521 |
Ligands and binding sites
- BR · Bromide ion · ion · 2 copies · chains A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, C
- IMD · Imidazole · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.77 | 0.96 | 20 | empty |
| 2 | 86 | 0.76 | 0.98 | 20 | MPD |
| 3 | 139 | 0.42 | 0.75 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3174 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 912 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 904 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 231 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5VWW · Bak core latch dimer in complex with Bim-RT - Tetragonal · the same entry in another collection · chain D against D, TM-score 1.00
- O43521 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 11 (O43521) · a predicted model of the same protein · chain C against A, TM-score 0.73
- Q16611 · AlphaFold monomer V2.0 prediction for BCL-2 homologous ANTAGONIST/KILLER (Q16611) · a predicted model of the same protein · chain A 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
- Every structure of UniProt O43521
- Elsewhere: RCSB PDB 5VWW · PDBe 5VWW · UniProt Q16611 · UniProt O43521
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