Research workbench
Bak core latch dimer in complex with bim-H3PC-rt
Analyse Bak core latch dimer in complex with bim-H3PC-rt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VWY
- Type
- protein
- Length
- 178 residues
- Chains
- 2
- 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
- PO4
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2 homologous ANTAGONIST/KILLER | protein | 153 | 75% helix, 0% strand | Q16611 |
| B | BCL-2-like protein 11 | protein | 25 | 80% helix, 0% strand | O43521 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.40 | 0.79 | 12 | empty |
| 2 | 78 | 0.34 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1149 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 5VWY · Bak core latch dimer in complex with Bim-h3Pc-RT · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.81
- 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 0.72
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 5VWY · PDBe 5VWY · UniProt Q16611 · UniProt O43521
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