Research workbench
Cryo-EM structure of the NA+,K+-ATPase in the E2.2K+ state after addition of ATP
Analyse Cryo-EM structure of the NA+,K+-ATPase in the E2.2K+ state after addition of ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Y46
- Type
- protein
- Length
- 2,654 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Na, K-ATPase alpha subunit; NA+,K+-ATPase beta subunit; Fxyd domain-containing ion…
- UniProt
- Q4H132, C4IX13, Q70Q12
- Ligands
- CLR, ATP, PCW, NAG, MAN, BMA, FUC, K
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Na, K-ATPase alpha subunit | protein | 993 | 48% helix, 15% strand | Q4H132 |
| D, B | NA+,K+-ATPase beta subunit | protein | 294 | 21% helix, 20% strand | C4IX13 |
| E, G | Fxyd domain-containing ion transport regulator | protein | 40 | 68% helix, 0% strand | Q70Q12 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 8 copies · chains C, E, D, A, G, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, A
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains C, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains D, B
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains D, B
- BMA · beta-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains D, B
- K · Potassium ion · metal · 6 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.77 | 0.81 | 53 | empty |
| 2 | 855 | 0.77 | 0.80 | 56 | empty |
| 3 | 894 | 0.73 | 0.77 | 85 | K |
| 4 | 1197 | 0.73 | 0.76 | 109 | ATP |
| 5 | 830 | 0.71 | 0.77 | 73 | ATP |
Interfaces
8 interfaces between chains.
- C–D · 2116 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 2107 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 794 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 793 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 533 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 7Y46 · Cryo-EM structure of the Na+,K+-ATPase in the E2.2K+ state after addition of ATP · the same entry in another collection · chain C against C, 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 7Y46 · PDBe 7Y46 · UniProt Q4H132 · UniProt C4IX13 · UniProt Q70Q12
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