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Crystal structure of the high affinity complex between ouabain and the E2P form of the sodium-potassium pump
Analyse Crystal structure of the high affinity complex between ouabain and the E2P form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N23
- Type
- protein
- Length
- 2,574 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
- OBN, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% 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 | 992 | 46% helix, 15% strand | P05024 |
| B, D | SODIUM/POTASSIUM-transporting ATPase subunit beta-1 | protein | 264 | 17% helix, 16% strand | P05027 |
| G, E | NA+/K+ ATPase gamma subunit transcript variant a | protein | 31 | 65% helix, 0% strand | Q58K79 |
Ligands and binding sites
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 | 1069 | 0.78 | 0.80 | 92 | OBN |
| 2 | 732 | 0.77 | 0.81 | 61 | OBN |
| 3 | 88 | 0.76 | 0.97 | 25 | empty |
| 4 | 86 | 0.75 | 0.97 | 24 | empty |
| 5 | 842 | 0.73 | 0.77 | 65 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2094 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2062 Ų buried · 26 hydrogen bonds · protein-protein
- A–G · 701 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 692 Ų buried · 2 hydrogen bonds · protein-protein
- B–G · 306 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, phosphorylation).
Compared structures
- 3N23 · Crystal structure of the high affinity complex between ouabain and the E2P form of the… · 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 C 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 3N23 · PDBe 3N23 · UniProt P05024 · UniProt P05027 · UniProt Q58K79
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