MolNFT v1 · #186989 · protein
AFTMEM16 in C22 lipid nanodiscs with MSP1E3 scaffold protein in the presnece of CA2+
7RX2 · AFTMEM16 lipid scramblase: “AFTMEM16 in C22 lipid nanodiscs with MSP1E3 scaffold protein in the presnece of CA2+”. Electron microscopy, 2 ligands (PGW, CA), 18 pockets (best druggability 0.77). MolNFT v1 #186989 on GenesisL1: 3D…
- PDB
- 7RX2
- Type
- protein
- Length
- 1,230 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AFTMEM16 lipid scramblase
- UniProt
- Q4WA18
- Ligands
- PGW, CA
- Pockets
- 18 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | AFTMEM16 lipid scramblase | protein | 615 | 64% 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 · 14 copies · chains B, A
- CA · Calcium ion · metal · 4 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 | 815 | 0.77 | 0.81 | 74 | empty |
| 2 | 771 | 0.76 | 0.81 | 71 | empty |
| 3 | 776 | 0.70 | 0.76 | 54 | empty |
| 4 | 776 | 0.70 | 0.76 | 54 | empty |
| 5 | 292 | 0.62 | 0.79 | 47 | PGW |
Interfaces
1 interface between chains.
- B–A · 3999 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 7RX2 · afTMEM16 in C22 lipid nanodiscs with MSP1E3 scaffold protein in the presnece 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 7RX2 · PDBe 7RX2 · UniProt Q4WA18
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