Research workbench
Crystal structure of the sodium-potassium pump with bound potassium and ouabain
Analyse Crystal structure of the sodium-potassium pump with bound potassium and ouabain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A3Y
- Type
- protein
- Length
- 1,295 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Na, K-ATPase alpha subunit; NA+,K+-ATPase beta subunit; Phospholemman-like protein
- UniProt
- Q4H132, Q70Q12
- Ligands
- MF4, OBN, CLR, NAG, K, MG
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Na, K-ATPase alpha subunit | protein | 992 | 47% helix, 15% strand | Q4H132 |
| B | NA+,K+-ATPase beta subunit | protein | 265 | 18% helix, 19% strand | — |
| G | Phospholemman-like protein | protein | 38 | 68% helix, 0% strand | Q70Q12 |
Ligands and binding sites
- MF4 · Tetrafluoromagnesate(2-) · ligand · chains A
- OBN · Ouabain · ligand · chains A
- CLR · Cholesterol · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
- K · Potassium ion · metal · 3 copies · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.77 | 0.80 | 72 | OBN |
| 2 | 589 | 0.74 | 0.81 | 72 | K |
| 3 | 582 | 0.66 | 0.76 | 64 | empty |
| 4 | 116 | 0.62 | 0.87 | 22 | empty |
| 5 | 359 | 0.62 | 0.78 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2050 Ų buried · 26 hydrogen bonds · protein-protein
- A–G · 812 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 530 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3A3Y · Crystal structure of the sodium-potassium pump with bound potassium and ouabain · 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 Q70Q12
- Elsewhere: RCSB PDB 3A3Y · PDBe 3A3Y · UniProt Q4H132 · UniProt Q70Q12
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