Research workbench
Crystal structure of the NA,K-ATPase from bovine
Analyse Crystal structure of the NA,K-ATPase from bovine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XE5
- Type
- protein
- Length
- 1,308 residues
- Chains
- 3
- 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
- Q08DA1, G3MWR4, Q04645
- Ligands
- CLR, OBN, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 43% 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 | 995 | 48% helix, 14% strand | Q08DA1 |
| B | SODIUM/POTASSIUM-transporting ATPase subunit beta | protein | 281 | 20% helix, 19% strand | G3MWR4 |
| G | SODIUM/POTASSIUM-transporting ATPase subunit gamma | protein | 32 | 72% helix, 0% strand | Q04645 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A, B, G
- OBN · Ouabain · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.79 | 0.83 | 57 | OBN |
| 2 | 819 | 0.73 | 0.78 | 82 | empty |
| 3 | 234 | 0.70 | 0.86 | 30 | empty |
| 4 | 183 | 0.66 | 0.85 | 29 | empty |
| 5 | 288 | 0.57 | 0.77 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2090 Ų buried · 21 hydrogen bonds · protein-protein
- A–G · 798 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 290 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 4XE5 · Crystal structure of the Na,K-ATPase from bovine · the same entry in another collection · chain A against A, TM-score 1.00
- Q08DA1 · 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
- Q04645 · AlphaFold monomer V2.0 prediction for SODIUM/POTASSIUM-transporting ATPase subunit gamma… · a predicted model of the same protein · chain G against A, TM-score 0.86
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 Q08DA1
- Every structure of UniProt G3MWR4
- Every structure of UniProt Q04645
- Elsewhere: RCSB PDB 4XE5 · PDBe 4XE5 · UniProt Q08DA1 · UniProt G3MWR4 · UniProt Q04645
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