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Crystal structure of a na+-bound NA+,K+-ATPase preceding the E1P state with oligomycin
Analyse Crystal structure of a na+-bound NA+,K+-ATPase preceding the E1P state with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WGV
- Type
- protein
- Length
- 2,663 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
- I7HD36, P05027, Q58K79
- Ligands
- PC1, CLR, ALF, ADP, EFO, NAG, NA, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | SODIUM/POTASSIUM-transporting ATPase subunit alpha-1 (EC 3.6.3.9) | protein | 994 | 49% helix, 15% strand | I7HD36 |
| B, D | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 303 | 20% helix, 17% strand | P05027 |
| G | NA+/K+ ATPase gamma subunit transcript variant a | protein | 34 | 68% helix, 0% strand | Q58K79 |
| E | NA+/K+ ATPase gamma subunit transcript variant a | protein | 35 | 66% helix, 0% strand | Q58K79 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 10 copies · chains A, B, G, C, D, E
- CLR · Cholesterol · ligand · 6 copies · chains A, B, G, C, D, E
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, C
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- EFO · Oligomycin A · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
- NA · Sodium ion · metal · 8 copies · chains A, C
- MG · Magnesium ion · metal · 4 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 | 885 | 0.83 | 0.85 | 96 | MG, ALF, ADP |
| 2 | 1067 | 0.82 | 0.83 | 98 | MG, ALF, ADP |
| 3 | 882 | 0.74 | 0.78 | 66 | empty |
| 4 | 782 | 0.72 | 0.78 | 67 | empty |
| 5 | 50 | 0.70 | 0.97 | 12 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2351 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2348 Ų buried · 34 hydrogen bonds · protein-protein
- A–G · 765 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 726 Ų buried · 2 hydrogen bonds · protein-protein
- B–G · 287 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3WGV · Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state with oligomycin · the same entry in another collection · chain G against G, 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 D against A, TM-score 0.91
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 I7HD36
- Every structure of UniProt P05027
- Every structure of UniProt Q58K79
- Elsewhere: RCSB PDB 3WGV · PDBe 3WGV · UniProt I7HD36 · UniProt P05027 · UniProt Q58K79
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