MolNFT v1 · #69027 · protein
Crystal structure of the sodium-potassium pump
3KDP · SODIUM/POTASSIUM-transporting ATPase subunit alpha-1: “Crystal structure of the sodium-potassium pump”. X-ray diffraction, 4 ligands (MF4, CLR, RB), 20 pockets (best druggability 0.78). MolNFT v1 #69027 on GenesisL1: 3D structure…
- PDB
- 3KDP
- Type
- protein
- Length
- 2,622 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, CLR, RB, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 13% 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 | 43% helix, 14% strand | P05024 |
| B, D | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 286 | 14% helix, 10% strand | P05027 |
| G, H | NA+/K+ ATPase gamma subunit transcript variant a | protein | 27 | 81% helix, 0% strand | Q58K79 |
Ligands and binding sites
- MF4 · Tetrafluoromagnesate(2-) · ligand · 2 copies · chains A, C
- CLR · Cholesterol · 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.78 | 0.81 | 65 | empty |
| 2 | 818 | 0.78 | 0.81 | 61 | empty |
| 3 | 209 | 0.77 | 0.91 | 42 | empty |
| 4 | 82 | 0.71 | 0.95 | 25 | empty |
| 5 | 646 | 0.71 | 0.79 | 70 | RB |
Interfaces
7 interfaces between chains.
- C–D · 2017 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2011 Ų buried · 21 hydrogen bonds · protein-protein
- C–H · 735 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 721 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 242 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3KDP · Crystal structure of the sodium-potassium pump · the same entry in another collection · chain H against H, 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 0.97
- P05027 · AlphaFold monomer V2.0 prediction for SODIUM/POTASSIUM-transporting ATPase subunit beta-1… · a predicted model of the same protein · chain D against A, TM-score 0.93
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 3KDP · PDBe 3KDP · UniProt P05024 · UniProt P05027 · UniProt Q58K79
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