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NA,K-ATPase in the E2P state with bound ouabain and MG2+ in the cation-binding site
Analyse NA,K-ATPase in the E2P state with bound ouabain and MG2+ in the cation-binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HYT
- 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
- 3.6.3.9
- UniProt
- P05024, P05027, Q58K79
- Ligands
- 17F, CLR, OBN, CE1, 1AT, 1DS, NAG, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 16% 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 | 289 | 19% helix, 20% 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 | 287 | 19% helix, 20% strand | P05027 |
Ligands and binding sites
- 17F · O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine · ligand · 5 copies · chains A, B, G, C, E, D
- CLR · Cholesterol · ligand · 4 copies · chains A, B, C, G, D, E
- OBN · Ouabain · ligand · 2 copies · chains A, C
- CE1 · O-dodecanyl octaethylene glycol · ligand · 2 copies · chains A, B, G, C, E
- 1AT · beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside · ligand · chains A, C, D, E
- 1DS · 1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside · ligand · chains A, B, G, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, D
- 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.78 | 0.81 | 76 | OBN |
| 2 | 744 | 0.78 | 0.82 | 60 | OBN |
| 3 | 796 | 0.73 | 0.78 | 62 | MG |
| 4 | 805 | 0.73 | 0.78 | 64 | MG |
| 5 | 812 | 0.71 | 0.77 | 77 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2089 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2068 Ų buried · 26 hydrogen bonds · protein-protein
- A–G · 785 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 783 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 295 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan, 2 modified (disulfide, N-glycosylation, phosphorylation).
Compared structures
- 4HYT · Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site · the same entry in another collection · chain B against B, 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 D against A, TM-score 0.96
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 4HYT · PDBe 4HYT · UniProt P05024 · UniProt P05027 · UniProt Q58K79
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