Research workbench
Bak in complex with bim-H3GLG
Analyse Bak in complex with bim-H3GLG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VX0
- Type
- protein
- Length
- 379 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
- MG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2 homologous ANTAGONIST/KILLER | protein | 169 | 70% helix, 0% strand | Q16611 |
| B | BCL-2-like protein 11 | protein | 25 | 80% helix, 0% strand | O43521 |
| C | BCL-2 homologous ANTAGONIST/KILLER | protein | 161 | 72% helix, 0% strand | Q16611 |
| D | BCL-2-like protein 11 | protein | 24 | 83% helix, 0% strand | O43521 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.77 | 0.95 | 33 | empty |
| 2 | 74 | 0.45 | 0.82 | 18 | empty |
| 3 | 81 | 0.35 | 0.76 | 16 | MG |
Interfaces
3 interfaces between chains.
- A–B · 1317 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1306 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1020 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5VX0 · Bak in complex with Bim-h3Glg · 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 0.95
- O43521 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 11 (O43521) · a predicted model of the same protein · chain B against A, TM-score 0.80
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 5VX0 · PDBe 5VX0 · UniProt Q16611 · UniProt O43521
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.