MolNFT v1 · #67570 · protein
BIML12F in complex with BCL-xl
3IO8 · BCL-2-like protein 1: “BIML12F in complex with BCL-xl”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.68). MolNFT v1 #67570 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IO8
- Type
- protein
- Length
- 330 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 11
- UniProt
- Q07817, O43521
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2-like protein 1 | protein | 142 | 74% helix, 0% strand | Q07817 |
| B | BCL-2-like protein 11 | protein | 23 | 87% helix, 0% strand | O43521 |
| C | BCL-2-like protein 1 | protein | 146 | 76% helix, 0% strand | Q07817 |
| D | BCL-2-like protein 11 | protein | 19 | 89% helix, 0% strand | O43521 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.68 | 0.92 | 20 | empty |
| 2 | 227 | 0.59 | 0.80 | 30 | empty |
| 3 | 108 | 0.46 | 0.79 | 17 | empty |
| 4 | 71 | 0.40 | 0.79 | 12 | empty |
| 5 | 59 | 0.33 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2238 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1037 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 957 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3IO8 · BimL12F in complex with Bcl-xL · the same entry in another collection · chain D against D, 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 0.77
- 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 0.66
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 3IO8 · PDBe 3IO8 · UniProt Q07817 · UniProt O43521
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