Research workbench
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2PI-pl state)
Analyse Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2PI-pl state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K7M
- Type
- protein
- Length
- 1,307 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
- ALF, Y01, D39, NAG, MAN, MG
- Pockets
- 12 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase (EC 7.6.2.1) | protein | 983 | 45% helix, 16% strand | Q59EX4 |
| C | Cell cycle control protein 50A | protein | 324 | 29% helix, 20% strand | Q9NV96 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- Y01 · Cholesterol hemisuccinate · ligand · chains A, C
- D39 · (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid · 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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.82 | 0.83 | 88 | empty |
| 2 | 1022 | 0.77 | 0.79 | 100 | empty |
| 3 | 841 | 0.75 | 0.79 | 61 | empty |
| 4 | 375 | 0.69 | 0.82 | 39 | empty |
| 5 | 189 | 0.61 | 0.82 | 36 | D39 |
Interfaces
1 interface between chains.
- A–C · 3986 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6K7M · Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2Pi-PL 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 6K7M · PDBe 6K7M · UniProt Q59EX4 · UniProt Q9NV96
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.