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Crystal structure of the NA+,K+-ATPase in the E2P state with bound MG2+ (P4(3)2(1)2 symmetry)
Analyse Crystal structure of the NA+,K+-ATPase in the E2P state with bound MG2+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D91
- Type
- protein
- Length
- 1,319 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
- 7.2.2.13
- UniProt
- P05024, P05027, Q58K79
- Ligands
- PCW, CLR, NAG, MG
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SODIUM/POTASSIUM-transporting ATPase subunit alpha-1 (EC 7.2.2.13) | protein | 996 | 49% helix, 14% strand | P05024 |
| B | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 291 | 24% helix, 19% strand | P05027 |
| G | Fxyd domain-containing ion transport regulator | protein | 32 | 72% helix, 0% strand | Q58K79 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 11 copies · chains A, B
- CLR · Cholesterol · ligand · 2 copies · chains A, B, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
- MG · Magnesium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.78 | 0.79 | 92 | PCW |
| 2 | 1161 | 0.77 | 0.79 | 107 | empty |
| 3 | 548 | 0.63 | 0.75 | 62 | PCW |
| 4 | 158 | 0.62 | 0.85 | 29 | empty |
| 5 | 274 | 0.58 | 0.78 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2194 Ų buried · 21 hydrogen bonds · protein-protein
- A–G · 780 Ų buried · 2 hydrogen bonds · protein-protein
- B–G · 310 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 7D91 · Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ (P4(3)2(1)2… · 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 A against A, TM-score 0.97
- 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 0.97
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 7D91 · PDBe 7D91 · UniProt P05024 · UniProt P05027 · UniProt Q58K79
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