Research workbench
BCL-xl complex with beclin 1 BH3 domain T108D
Analyse BCL-xl complex with beclin 1 BH3 domain T108D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DCO
- Type
- protein
- Length
- 333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2-like protein 1,BCL-2-like protein 1; Beclin-1
- UniProt
- Q07817, Q14457
- Ligands
- CL
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | BCL-2-like protein 1,BCL-2-like protein 1 | protein | 146 | 71% helix, 0% strand | Q07817 |
| C | Beclin-1 | protein | 20 | 90% helix, 0% strand | Q14457 |
| D | Beclin-1 | protein | 21 | 86% helix, 0% strand | Q14457 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A
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 | 390 | 0.63 | 0.78 | 45 | CL |
| 2 | 62 | 0.48 | 0.85 | 12 | empty |
| 3 | 102 | 0.48 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2266 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 970 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 871 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6DCO · Bcl-xL complex with Beclin 1 BH3 domain T108D · the same entry in another collection · chain D against D, TM-score 1.00
- Q14457 · AlphaFold monomer V2.0 prediction for beclin-1 (Q14457) · a predicted model of the same protein · chain C against A, TM-score 0.83
- Q07817 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 1 (Q07817) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 Q07817
- Every structure of UniProt Q14457
- Elsewhere: RCSB PDB 6DCO · PDBe 6DCO · UniProt Q07817 · UniProt Q14457
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