Research workbench
Cryo-EM structure of a human ATP11C-CDC50A flippase in ptdser-occluded E2-alf state
Analyse Cryo-EM structure of a human ATP11C-CDC50A flippase in ptdser-occluded E2-alf… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BSV
- Type
- protein
- Length
- 1,139 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP11C; CDC50A
- Ligands
- ALF, P5S, NAG, MAN, MG
- Pockets
- 14 · best druggability 0.77
Structure
electron microscopy · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP11C | protein | 815 | 46% helix, 12% strand | — |
| C | CDC50A | protein | 324 | 25% helix, 20% strand | — |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · chains C
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.77 | 0.84 | 56 | empty |
| 2 | 346 | 0.68 | 0.82 | 44 | empty |
| 3 | 101 | 0.68 | 0.91 | 27 | empty |
| 4 | 595 | 0.68 | 0.77 | 54 | empty |
| 5 | 165 | 0.62 | 0.84 | 27 | P5S |
Interfaces
1 interface between chains.
- A–C · 4069 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7BSV · Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-occluded E2-AlF state · 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
- Elsewhere: RCSB PDB 7BSV · PDBe 7BSV
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