MolNFT v1 · #154319 · protein
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ADP- pi state)
6K7K · Phospholipid-transporting ATPase: “Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ADP- pi state)”. Electron microscopy, 6 ligands (ADP, ALF, Y01), 14 pockets (best druggability 0.77). MolNFT v1 #154319 on…
- PDB
- 6K7K
- Type
- protein
- Length
- 1,309 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipid-transporting ATPase; Cell cycle control protein 50A
- EC
- 7.6.2.1
- UniProt
- Q59EX4, Q9NV96
- Ligands
- ADP, ALF, Y01, NAG, MAN, MG
- Pockets
- 14 · best druggability 0.77
Structure
electron microscopy · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase (EC 7.6.2.1) | protein | 984 | 46% helix, 16% strand | Q59EX4 |
| C | Cell cycle control protein 50A | protein | 325 | 30% helix, 21% strand | Q9NV96 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- Y01 · Cholesterol hemisuccinate · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar
- MG · Magnesium ion · metal · 2 copies · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.77 | 0.79 | 99 | ADP, ALF, MG |
| 2 | 782 | 0.73 | 0.78 | 63 | empty |
| 3 | 868 | 0.71 | 0.76 | 76 | empty |
| 4 | 385 | 0.68 | 0.81 | 42 | empty |
| 5 | 54 | 0.68 | 0.97 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 4081 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6K7K · Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ADP-Pi state) · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.95
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 Q59EX4
- Every structure of UniProt Q9NV96
- Elsewhere: RCSB PDB 6K7K · PDBe 6K7K · UniProt Q59EX4 · UniProt Q9NV96
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