MolNFT v1 · #154318 · protein
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ATP state CLASS1)
6K7J · Phospholipid-transporting ATPase: “Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ATP state CLASS1)”. Electron microscopy, 5 ligands (ACP, Y01, NAG), 14 pockets (best druggability 0.78). MolNFT v1 #154318 on…
- PDB
- 6K7J
- Type
- protein
- Length
- 1,311 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
- ACP, Y01, NAG, MAN, MG
- Pockets
- 14 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase (EC 7.6.2.1) | protein | 986 | 44% helix, 14% strand | Q59EX4 |
| C | Cell cycle control protein 50A | protein | 325 | 28% helix, 19% strand | Q9NV96 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · 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 · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.78 | 0.80 | 86 | ACP, MG |
| 2 | 890 | 0.75 | 0.79 | 79 | empty |
| 3 | 93 | 0.72 | 0.94 | 21 | empty |
| 4 | 301 | 0.71 | 0.85 | 43 | empty |
| 5 | 548 | 0.71 | 0.80 | 38 | empty |
Interfaces
1 interface between chains.
- A–C · 3953 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6K7J · Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ATP state class1) · 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 6K7J · PDBe 6K7J · UniProt Q59EX4 · UniProt Q9NV96
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