Research workbench
Crystal structures of NA+,K+-ATPase in complex with beryllium fluoride
Analyse Crystal structures of NA+,K+-ATPase in complex with beryllium fluoride in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DDF
- Type
- protein
- Length
- 2,632 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
- 7.2.2.13
- UniProt
- P05024, P05027, Q58K79
- Ligands
- PCW, CLR, NAG, MG, NA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | SODIUM/POTASSIUM-transporting ATPase subunit alpha-1 (EC 7.2.2.13) | protein | 996 | 48% helix, 15% strand | P05024 |
| B | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 291 | 22% helix, 19% strand | P05027 |
| G, E | Fxyd domain-containing ion transport regulator | protein | 32 | 72% helix, 0% strand | Q58K79 |
| D | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 285 | 23% helix, 19% strand | P05027 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 8 copies · chains A, B, C, D, E, G
- CLR · Cholesterol · ligand · 6 copies · chains A, B, C, G, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C
- NA · Sodium ion · metal · 2 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.79 | 0.82 | 64 | empty |
| 2 | 847 | 0.79 | 0.81 | 64 | empty |
| 3 | 916 | 0.76 | 0.79 | 71 | NA |
| 4 | 885 | 0.75 | 0.79 | 93 | NA |
| 5 | 580 | 0.72 | 0.80 | 61 | PCW, CLR |
Interfaces
10 interfaces between chains.
- A–B · 2190 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2181 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 798 Ų buried · 4 hydrogen bonds · protein-protein
- A–G · 783 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 291 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 7DDF · Crystal structures of Na+,K+-ATPase in complex with beryllium fluoride · the same entry in another collection · chain E against E, 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 0.98
- 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 0.98
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 7DDF · PDBe 7DDF · UniProt P05024 · UniProt P05027 · UniProt Q58K79
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