Research workbench
Cryo EM structure of a na+-bound NA+,K+-ATPase in the E1 state with ATP-gamma-S
Analyse Cryo EM structure of a na+-bound NA+,K+-ATPase in the E1 state with ATP-gamma-S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E21
- Type
- protein
- Length
- 1,302 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SODIUM/POTASSIUM-transporting ATPase subunit alpha-1; SODIUM/POTASSIUM-transporting…
- EC
- 7.2.2.13
- UniProt
- P05023, P05026, P54710
- Ligands
- Y01, PC1, AGS, NAG, NA, MG
- Pockets
- 18 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SODIUM/POTASSIUM-transporting ATPase subunit alpha-1 (EC 7.2.2.13) | protein | 976 | 42% helix, 13% strand | P05023 |
| B | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 294 | 18% helix, 20% strand | P05026 |
| C | SODIUM/POTASSIUM-transporting ATPase subunit gamma | protein | 32 | 69% helix, 0% strand | P54710 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 6 copies · chains A, B, C
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
- NA · Sodium ion · metal · 4 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
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.77 | 0.87 | 40 | NA |
| 2 | 617 | 0.76 | 0.82 | 47 | empty |
| 3 | 635 | 0.71 | 0.79 | 59 | MG, AGS |
| 4 | 175 | 0.58 | 0.82 | 26 | empty |
| 5 | 260 | 0.54 | 0.76 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2185 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 786 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 282 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7E21 · Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S · the same entry in another collection · chain A against A, TM-score 1.00
- P05026 · 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 0.97
- P54710 · AlphaFold monomer V2.0 prediction for SODIUM/POTASSIUM-transporting ATPase subunit gamma… · a predicted model of the same protein · chain C against A, TM-score 0.84
- P05023 · AlphaFold monomer V2.0 prediction for SODIUM/POTASSIUM-transporting ATPase subunit… · a predicted model of the same protein · chain A against A, TM-score 0.66
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 P05023
- Every structure of UniProt P05026
- Every structure of UniProt P54710
- Elsewhere: RCSB PDB 7E21 · PDBe 7E21 · UniProt P05023 · UniProt P05026 · UniProt P54710
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