Research workbench
Structure of A6 reveals a novel lipid transporter
Analyse Structure of A6 reveals a novel lipid transporter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BR8
- Type
- protein
- Length
- 498 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein A6 homolog
- UniProt
- Q9J563
- Ligands
- 6OU, PGV
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein A6 homolog | protein | 249 | 77% helix, 3% strand | Q9J563 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 8 copies · chains A, B
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.62 | 0.74 | 46 | 6OU |
| 2 | 479 | 0.61 | 0.74 | 42 | 6OU |
| 3 | 495 | 0.61 | 0.74 | 48 | empty |
| 4 | 236 | 0.56 | 0.78 | 31 | empty |
| 5 | 325 | 0.55 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 523 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 6BR8 · Structure of A6 reveals a novel lipid transporter · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9J563
- Elsewhere: RCSB PDB 6BR8 · PDBe 6BR8 · UniProt Q9J563
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.