Research workbench
Crystal structure of the sodium-potassium pump
Analyse Crystal structure of the sodium-potassium pump in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B8E
- Type
- protein
- Length
- 2,146 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SODIUM/POTASSIUM-transporting ATPase subunit alpha-1; SODIUM/POTASSIUM-transporting…
- EC
- 3.6.3.9
- UniProt
- P05024, P05027, Q58K79
- Ligands
- MF4, PC1, RB, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | SODIUM/POTASSIUM-transporting ATPase subunit alpha-1 (EC 3.6.3.9) | protein | 998 | 40% helix, 13% strand | P05024 |
| B, D | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 46 | 54% helix, 0% strand | P05027 |
| G, H | NA+/K+ ATPase gamma subunit transcript variant a | protein | 29 | 14% helix, 0% strand | Q58K79 |
Ligands and binding sites
- MF4 · Tetrafluoromagnesate(2-) · ligand · 2 copies · chains A, C
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B, C, D
- RB · Rubidium ion · metal · 6 copies · chains A, C
- MG · Magnesium 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.74 | 0.79 | 51 | empty |
| 2 | 736 | 0.73 | 0.79 | 57 | empty |
| 3 | 519 | 0.69 | 0.79 | 68 | RB |
| 4 | 673 | 0.66 | 0.75 | 88 | empty |
| 5 | 149 | 0.66 | 0.87 | 30 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1126 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1063 Ų buried · 15 hydrogen bonds · protein-protein
- C–H · 762 Ų buried · 0 hydrogen bonds · protein-protein
- A–G · 665 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 253 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3B8E · Crystal structure of the sodium-potassium pump · the same entry in another collection · chain D against D, TM-score 1.00
- P05024 · AlphaFold monomer V2.0 prediction for SODIUM/POTASSIUM-transporting ATPase subunit… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P05027 · AlphaFold monomer V2.0 prediction for SODIUM/POTASSIUM-transporting ATPase subunit beta-1… · a predicted model of the same protein · chain B against A, TM-score 0.78
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 P05024
- Every structure of UniProt P05027
- Every structure of UniProt Q58K79
- Elsewhere: RCSB PDB 3B8E · PDBe 3B8E · UniProt P05024 · UniProt P05027 · UniProt Q58K79
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