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Cryo-EM structure of NA+,K+-ATPase in the E2P state formed by ATP with istaroxime
Analyse Cryo-EM structure of NA+,K+-ATPase in the E2P state formed by ATP with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WYX
- Type
- protein
- Length
- 2,654 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SODIUM/POTASSIUM-transporting ATPase subunit alpha; NA+,K+-ATPase beta subunit; Fxyd…
- UniProt
- Q4H132, C4IX13, Q70Q12
- Ligands
- PCW, CLR, ATP, 7Q2, NAG, MAN, BMA, FUC, MG, NA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | SODIUM/POTASSIUM-transporting ATPase subunit alpha | protein | 993 | 49% helix, 15% strand | Q4H132 |
| B, D | NA+,K+-ATPase beta subunit | protein | 294 | 21% helix, 22% strand | C4IX13 |
| G, E | Fxyd domain-containing ion transport regulator | protein | 40 | 68% helix, 0% strand | Q70Q12 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 24 copies · chains A, G, B, C, D, E
- CLR · Cholesterol · ligand · 8 copies · chains A, B, C, G, D, E
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- 7Q2 · (3E,5S,8R,9S,10R,13S,14S)-3-(2-azanylethoxyimino)-10, 13-dimethyl-1,2,4,5,7,8,9,11,12,14,15,16-dodecahydrocyclopenta[a]phenanthrene-6,17-dione · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains B, D
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains B, D
- BMA · beta-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.79 | 0.81 | 77 | 7Q2 |
| 2 | 838 | 0.78 | 0.81 | 64 | 7Q2 |
| 3 | 1199 | 0.77 | 0.79 | 130 | NA |
| 4 | 547 | 0.72 | 0.80 | 56 | NA |
| 5 | 212 | 0.66 | 0.84 | 36 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2136 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2125 Ų buried · 20 hydrogen bonds · protein-protein
- A–G · 801 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 796 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 487 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide, 2 modified (N-glycosylation, disulfide, phosphorylation).
Compared structures
- 7WYX · Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP with istaroxime · 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
- Every structure of UniProt Q4H132
- Every structure of UniProt C4IX13
- Every structure of UniProt Q70Q12
- Elsewhere: RCSB PDB 7WYX · PDBe 7WYX · UniProt Q4H132 · UniProt C4IX13 · UniProt Q70Q12
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