MolNFT v1 · #94234 · protein
Crystal structure of NA+,K+-ATPase in the na+-bound state
4HQJ · SODIUM/POTASSIUM-transporting ATPase subunit alpha-1: “Crystal structure of NA+,K+-ATPase in the na+-bound state”. X-ray diffraction, 5 ligands (CLR, ADP, ALF), 20 pockets (best druggability 0.83). MolNFT v1 #94234 on GenesisL1: 3D…
- PDB
- 4HQJ
- Type
- protein
- Length
- 2,598 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
- CLR, ADP, ALF, NA, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SODIUM/POTASSIUM-transporting ATPase subunit alpha-1 (EC 3.6.3.9) | protein | 985 | 47% helix, 16% strand | P05024 |
| B, D | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 285 | 15% helix, 16% strand | P05027 |
| G | NA+/K+ ATPase gamma subunit transcript variant a | protein | 27 | 81% helix, 0% strand | Q58K79 |
| C | SODIUM/POTASSIUM-transporting ATPase subunit alpha-1 (EC 3.6.3.9) | protein | 987 | 47% helix, 16% strand | P05024 |
| E | NA+/K+ ATPase gamma subunit transcript variant a | protein | 29 | 76% helix, 0% strand | Q58K79 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 5 copies · chains A, G, B, C, E, D
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, C
- NA · Sodium 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.83 | 0.86 | 77 | ADP, ALF, MG |
| 2 | 1189 | 0.80 | 0.82 | 99 | ADP, ALF, MG |
| 3 | 80 | 0.73 | 0.96 | 24 | empty |
| 4 | 536 | 0.73 | 0.81 | 57 | empty |
| 5 | 507 | 0.72 | 0.81 | 56 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2062 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2005 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 750 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 716 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 242 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4HQJ · Crystal structure of Na+,K+-ATPase in the Na+-bound state · the same entry in another collection · chain E against E, TM-score 1.00
- 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 0.93
- P05024 · AlphaFold monomer V2.0 prediction for SODIUM/POTASSIUM-transporting ATPase subunit… · a predicted model of the same protein · chain C against A, TM-score 0.65
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 4HQJ · PDBe 4HQJ · UniProt P05024 · UniProt P05027 · UniProt Q58K79
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