Research workbench
Crystal structure of BCL-xl in complex with computationally designed inhibitor protein
Analyse Crystal structure of BCL-xl in complex with computationally designed inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XGG
- Type
- protein
- Length
- 910 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2-like protein 1; BCL-xl and mcl-1 dual inhibitor
- UniProt
- Q07817
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | BCL-2-like protein 1 | protein | 145 | 79% helix, 0% strand | Q07817 |
| A, D | BCL-xl and mcl-1 dual inhibitor | protein | 162 | 89% helix, 0% strand | — |
| F | BCL-2-like protein 1 | protein | 148 | 79% helix, 0% strand | Q07817 |
| C | BCL-2-like protein 1 | protein | 147 | 78% helix, 0% strand | Q07817 |
| E | BCL-2-like protein 1 | protein | 146 | 78% helix, 0% strand | Q07817 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.70 | 0.76 | 90 | empty |
| 2 | 64 | 0.58 | 0.90 | 13 | empty |
| 3 | 66 | 0.56 | 0.88 | 20 | empty |
| 4 | 145 | 0.54 | 0.81 | 26 | empty |
| 5 | 101 | 0.51 | 0.82 | 19 | empty |
Interfaces
7 interfaces between chains.
- B–A · 1474 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1378 Ų buried · 24 hydrogen bonds · protein-protein
- F–D · 1370 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1348 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 397 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 7XGG · Crystal structure of BCL-xL in complex with computationally designed inhibitor protein · the same entry in another collection · chain E against E, TM-score 1.00
- Q07817 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 1 (Q07817) · a predicted model of the same protein · chain C against A, TM-score 0.95
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
- Elsewhere: RCSB PDB 7XGG · PDBe 7XGG · UniProt Q07817
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