Research workbench
AFTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of CA2+
Analyse AFTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of CA2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RXA
- Type
- protein
- Length
- 1,156 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AFTMEM16 lipid scramblase
- UniProt
- Q4WA18
- Ligands
- PGW
- Pockets
- 19 · best druggability 0.74
Structure
electron microscopy · 1 distinct chain · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AFTMEM16 lipid scramblase | protein | 578 | 65% helix, 5% strand | Q4WA18 |
Ligands and binding sites
- PGW · (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.74 | 0.77 | 76 | empty |
| 2 | 926 | 0.73 | 0.77 | 64 | empty |
| 3 | 360 | 0.68 | 0.81 | 43 | empty |
| 4 | 362 | 0.67 | 0.80 | 41 | empty |
| 5 | 425 | 0.59 | 0.74 | 50 | PGW |
Interfaces
1 interface between chains.
- A–B · 2787 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7RXA · afTMEM16 DE/AA mutant in C14 lipid nanodiscs in the presence of Ca2+ · 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 Q4WA18
- Elsewhere: RCSB PDB 7RXA · PDBe 7RXA · UniProt Q4WA18
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