Research workbench
Cryo-EM structure of a human ATP11C-CDC50A flippase reconstituted in the nanodisc in ptdser-occluded E2-pi state.
Analyse Cryo-EM structure of a human ATP11C-CDC50A flippase reconstituted in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VSG
- Type
- protein
- Length
- 1,139 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipid-transporting ATPase ig; Cell cycle control protein 50A
- EC
- 7.6.2.1
- UniProt
- Q8NB49, Q9NV96
- Ligands
- 17F, NAG, MAN
- Pockets
- 16 · best druggability 0.76
Structure
electron microscopy · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase ig (EC 7.6.2.1) | protein | 815 | 50% helix, 11% strand | Q8NB49 |
| B | Cell cycle control protein 50A | protein | 324 | 30% helix, 18% strand | Q9NV96 |
Ligands and binding sites
- 17F · O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.76 | 0.88 | 31 | empty |
| 2 | 698 | 0.74 | 0.80 | 74 | empty |
| 3 | 195 | 0.73 | 0.89 | 29 | 17F |
| 4 | 632 | 0.71 | 0.78 | 52 | empty |
| 5 | 541 | 0.69 | 0.79 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 3991 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 7VSG · Cryo-EM structure of a human ATP11C-CDC50A flippase reconstituted in the Nanodisc in… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NV96 · AlphaFold monomer V2.0 prediction for cell cycle control protein 50A (Q9NV96) · a predicted model of the same protein · chain B against A, TM-score 0.93
- Q8NB49 · AlphaFold monomer V2.0 prediction for phospholipid-transporting ATPase ig (Q8NB49) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q8NB49
- Every structure of UniProt Q9NV96
- Elsewhere: RCSB PDB 7VSG · PDBe 7VSG · UniProt Q8NB49 · UniProt Q9NV96
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