MolNFT v1 · #113487 · protein
BCL-2 alpha beta-1 linear complex
5AGX · Apoptosis regulator BCL-2, BCL-2-like protein 1, apoptosis…: “BCL-2 alpha beta-1 linear complex”. X-ray diffraction, 1 ligand (ACE), 6 pockets (best druggability 0.59). MolNFT v1 #113487 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5AGX
- Type
- protein
- Length
- 323 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apoptosis regulator BCL-2, BCL-2-like protein 1, apoptosis regulator BCL-2; BCL-2-like…
- UniProt
- P10415, Q07817, O43521
- Ligands
- ACE
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apoptosis regulator BCL-2, BCL-2-like protein 1, apoptosis regulator BCL-2 | protein | 140 | 74% helix, 0% strand | P10415, Q07817 |
| B | Apoptosis regulator BCL-2, BCL-2-like protein 1, apoptosis regulator BCL-2 | protein | 141 | 76% helix, 0% strand | P10415, Q07817 |
| C, D | BCL-2-like protein 11 | protein | 21 | 76% helix, 0% strand | O43521 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.59 | 0.81 | 24 | empty |
| 2 | 108 | 0.58 | 0.85 | 20 | empty |
| 3 | 192 | 0.54 | 0.79 | 22 | empty |
| 4 | 138 | 0.49 | 0.79 | 21 | empty |
| 5 | 86 | 0.31 | 0.73 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1053 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 985 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 356 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 214 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 2 covalent (nonstandard, covalent ligand).
Compared structures
- 5AGX · Bcl-2 alpha beta-1 LINEAR complex · the same entry in another collection · chain B against B, TM-score 1.00
- P10415 · AlphaFold monomer V2.0 prediction for apoptosis regulator BCL-2 (P10415) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q07817 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 1 (Q07817) · a predicted model of the same protein · chain B against A, TM-score 0.95
- O43521 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 11 (O43521) · a predicted model of the same protein · chain D against A, TM-score 0.60
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 P10415
- Every structure of UniProt Q07817
- Every structure of UniProt O43521
- Elsewhere: RCSB PDB 5AGX · PDBe 5AGX · UniProt P10415 · UniProt Q07817 · UniProt O43521
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