MolNFT v1 · #137710 · protein
Bak core latch dimer in complex with bim-H0-H3GLT
5VWX · BCL-2 homologous ANTAGONIST/KILLER: “Bak core latch dimer in complex with bim-H0-H3GLT”. X-ray diffraction, 1 pocket (best druggability 0.63). MolNFT v1 #137710 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VWX
- Type
- protein
- Length
- 342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-2 homologous ANTAGONIST/KILLER; BCL-2-like protein 11
- UniProt
- Q16611, O43521
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-2 homologous ANTAGONIST/KILLER | protein | 148 | 80% helix, 0% strand | Q16611 |
| B, D | BCL-2-like protein 11 | protein | 23 | 91% helix, 0% strand | O43521 |
| C | BCL-2 homologous ANTAGONIST/KILLER | protein | 148 | 80% helix, 0% strand | Q16611 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.63 | 0.75 | 49 | EDO |
Interfaces
5 interfaces between chains.
- A–C · 3334 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1209 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1196 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 96 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5VWX · Bak core latch dimer in complex with Bim-h0-h3Glt · the same entry in another collection · chain D against D, TM-score 1.00
- 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 0.74
- Q16611 · AlphaFold monomer V2.0 prediction for BCL-2 homologous ANTAGONIST/KILLER (Q16611) · a predicted model of the same protein · chain C against A, TM-score 0.70
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 Q16611
- Every structure of UniProt O43521
- Elsewhere: RCSB PDB 5VWX · PDBe 5VWX · UniProt Q16611 · UniProt O43521
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