Research workbench
Structure of BCL-xl bound to bimlock
Analyse Structure of BCL-xl bound to bimlock in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YQ7
- Type
- protein
- Length
- 163 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2-like protein 1; BCL-2-like protein 11
- UniProt
- Q07817, O43521
- Ligands
- ACE, NH2
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2-like protein 1 | protein | 145 | 81% helix, 0% strand | Q07817 |
| B | BCL-2-like protein 11 | protein | 18 | 89% helix, 0% strand | O43521 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- NH2 · Amino group · ion · chains B
- GOL · Glycerol · additive · chains A
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 | 83 | 0.35 | 0.76 | 20 | GOL |
| 2 | 64 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 isopeptide (covalent ligand, isopeptide).
Compared structures
- 2YQ7 · Structure of Bcl-xL bound to BimLOCK · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.78
- 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 0.72
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 Q07817
- Every structure of UniProt O43521
- Elsewhere: RCSB PDB 2YQ7 · PDBe 2YQ7 · UniProt Q07817 · UniProt O43521
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