Research workbench
Crystal structure of Trichoplax adhaerens trBcl-2L2 bound to trBak BH3
Analyse Crystal structure of Trichoplax adhaerens trBcl-2L2 bound to trBak BH3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YLD
- Type
- protein
- Length
- 347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Trichoplax sp. H2; SYNTHETIC CONSTRUCT
- Molecule
- Bcl-2-like protein 1; Bcl-2 homologous antagonist/killer
- UniProt
- A0A369S2N9, A0A369S334
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · resolution 1.4 · 4 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bcl-2-like protein 1 | protein | 150 | 77% helix, 0% strand | A0A369S2N9 |
| B | Bcl-2 homologous antagonist/killer | protein | 24 | 88% helix, 0% strand | A0A369S334 |
| C | Bcl-2-like protein 1 | protein | 152 | 76% helix, 0% strand | A0A369S2N9 |
| D | Bcl-2 homologous antagonist/killer | protein | 21 | 81% helix, 0% strand | A0A369S334 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
- TAR · D(-)-tartaric acid · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.50 | 0.78 | 26 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1013 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 984 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 359 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 339 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YLD · Crystal structure of trichoplax adhaerens trbcl-2L2 bound to trbak BH3 · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A369S2N9
- Every structure of UniProt A0A369S334
- Elsewhere: RCSB PDB 6YLD · PDBe 6YLD · UniProt A0A369S2N9 · UniProt A0A369S334
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.