Research workbench
Crystal structure of the NA,K-ATPase E2P-digoxin complex with bound magnesium
Analyse Crystal structure of the NA,K-ATPase E2P-digoxin complex with bound magnesium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RET
- Type
- protein
- Length
- 2,634 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, 17F, DGX, NAG, GLC, FRU, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | SODIUM/POTASSIUM-transporting ATPase subunit alpha-1 (EC 3.6.3.9) | protein | 996 | 49% helix, 14% strand | P05024 |
| B | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 290 | 18% helix, 22% strand | P05027 |
| G, E | NA+/K+ ATPase gamma subunit transcript variant a | protein | 32 | 72% helix, 0% strand | Q58K79 |
| D | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 288 | 18% helix, 22% strand | P05027 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 4 copies · chains A, B, C, G, D, E
- 17F · O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine · ligand · 3 copies · chains A, B
- DGX · Digoxin · ligand · 2 copies · chains A, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, D
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B, G, C, D, E
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, C
- MG · Magnesium ion · metal · 6 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.79 | 0.82 | 79 | DGX |
| 2 | 850 | 0.78 | 0.81 | 75 | DGX |
| 3 | 650 | 0.75 | 0.81 | 66 | MG |
| 4 | 661 | 0.71 | 0.79 | 72 | empty |
| 5 | 623 | 0.71 | 0.79 | 75 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2115 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2096 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 779 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 777 Ų buried · 5 hydrogen bonds · protein-protein
- B–G · 296 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan, 2 modified (disulfide, N-glycosylation, phosphorylation).
Compared structures
- 4RET · Crystal structure of the Na,K-ATPase E2P-digoxin complex with bound magnesium · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.98
- 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 0.95
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 4RET · PDBe 4RET · UniProt P05024 · UniProt P05027 · UniProt Q58K79
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