MolNFT v1 · #137008 · protein
BCL-2 complex with beclin 1 T108D BH3 domain
5VAY · Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera: “BCL-2 complex with beclin 1 T108D BH3 domain”. X-ray diffraction, 7 pockets (best druggability 0.63). MolNFT v1 #137008 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VAY
- Type
- protein
- Length
- 654 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera; Beclin-1
- UniProt
- P10415, Q07817, Q14457
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 7 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera | protein | 151 | 70% helix, 0% strand | P10415, Q07817 |
| B | Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera | protein | 145 | 74% helix, 0% strand | P10415, Q07817 |
| C | Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera | protein | 139 | 75% helix, 0% strand | P10415, Q07817 |
| D | Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera | protein | 136 | 76% helix, 0% strand | P10415, Q07817 |
| E, F | Beclin-1 | protein | 21 | 90% helix, 0% strand | Q14457 |
| G | Beclin-1 | protein | 21 | 90% helix, 0% strand | Q14457 |
| H | Beclin-1 | protein | 20 | 85% helix, 0% strand | Q14457 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.63 | 0.81 | 33 | empty |
| 2 | 283 | 0.59 | 0.78 | 45 | empty |
| 3 | 148 | 0.55 | 0.81 | 25 | empty |
| 4 | 100 | 0.53 | 0.83 | 16 | empty |
| 5 | 95 | 0.46 | 0.80 | 18 | empty |
Interfaces
11 interfaces between chains.
- C–G · 1103 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 1045 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 1005 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 933 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 454 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5VAY · Bcl-2 complex with Beclin 1 T108D BH3 domain · the same entry in another collection · chain C against C, TM-score 1.00
- P10415 · AlphaFold monomer V2.0 prediction for apoptosis regulator BCL-2 (P10415) · a predicted model of the same protein · chain C 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 C against A, TM-score 0.96
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 Q14457
- Elsewhere: RCSB PDB 5VAY · PDBe 5VAY · UniProt P10415 · UniProt Q07817 · UniProt Q14457
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