MolNFT v1 · #187000 · protein
AFTMEM16 in C18 lipid nanodiscs with MSP1E3 scaffold protein in the presence of CA2+, monomer with extra lipids
7RXH · AFTMEM16 lipid scramblase: “AFTMEM16 in C18 lipid nanodiscs with MSP1E3 scaffold protein in the presence of CA2+, monomer with extra…”. Electron microscopy, 2 ligands (PGW, CA), 9 pockets (best druggability 0.76). MolNFT v1 #187000…
- PDB
- 7RXH
- Type
- protein
- Length
- 626 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AFTMEM16 lipid scramblase
- UniProt
- Q4WA18
- Ligands
- PGW, CA
- Pockets
- 9 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 66% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AFTMEM16 lipid scramblase | protein | 626 | 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 A
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.76 | 0.78 | 92 | empty |
| 2 | 761 | 0.70 | 0.76 | 47 | empty |
| 3 | 93 | 0.65 | 0.91 | 22 | empty |
| 4 | 114 | 0.48 | 0.79 | 17 | empty |
| 5 | 96 | 0.47 | 0.80 | 13 | empty |
Compared structures
- 7RXH · afTMEM16 in C18 lipid nanodiscs with MSP1E3 scaffold protein 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 7RXH · PDBe 7RXH · UniProt Q4WA18
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