Research workbench
afTMEM16 in C14 lipid nanodiscs with MSP1E3 scaffold protein in the absence of Ca2+
Analyse afTMEM16 in C14 lipid nanodiscs with MSP1E3 scaffold protein in the absence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RX3
- Type
- protein
- Length
- 1,182 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163)
- Molecule
- afTMEM16 lipid scramblase
- UniProt
- Q4WA18
- Ligands
- PGW
- Pockets
- 18 · best druggability 0.78
Structure
electron microscopy · resolution 3.3 · 1 distinct chain · 66% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | afTMEM16 lipid scramblase | protein | 591 | 66% helix, 6% 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 · 16 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.78 | 0.80 | 73 | empty |
| 2 | 953 | 0.76 | 0.79 | 68 | empty |
| 3 | 489 | 0.75 | 0.83 | 47 | empty |
| 4 | 475 | 0.74 | 0.82 | 49 | empty |
| 5 | 777 | 0.66 | 0.73 | 82 | PGW |
Interfaces
1 interface between chains.
- B–A · 3469 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7RX3 · AFTMEM16 in C14 lipid nanodiscs with MSP1E3 scaffold protein in the absence 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 7RX3 · PDBe 7RX3 · UniProt Q4WA18
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