Research workbench
Cryo-EM structure of gastric H+,K+-ATPase with bound rubidium
Analyse Cryo-EM structure of gastric H+,K+-ATPase with bound rubidium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YN9
- Type
- protein
- Length
- 1,239 residues
- Chains
- 2
- Method
- electron crystallography
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium-transporting ATPase alpha chain 1; Potassium-transporting ATPase subunit beta
- EC
- 3.6.3.10
- UniProt
- P19156, P18434
- Pockets
- 16 · best druggability 0.78
Structure
electron crystallography · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium-transporting ATPase alpha chain 1 (EC 3.6.3.10) | protein | 993 | 50% helix, 15% strand | P19156 |
| B | Potassium-transporting ATPase subunit beta | protein | 246 | 20% helix, 17% strand | P18434 |
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.78 | 0.83 | 84 | empty |
| 2 | 917 | 0.74 | 0.77 | 70 | empty |
| 3 | 465 | 0.69 | 0.80 | 59 | empty |
| 4 | 381 | 0.64 | 0.79 | 66 | empty |
| 5 | 263 | 0.61 | 0.80 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2082 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2YN9 · Cryo-EM structure of gastric H+,K+-ATPase with bound rubidium · the same entry in another collection · chain A against A, TM-score 1.00
- P19156 · AlphaFold monomer V2.0 prediction for potassium-transporting ATPase alpha chain 1 (P19156) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P18434 · AlphaFold monomer V2.0 prediction for potassium-transporting ATPase subunit beta (P18434) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P19156
- Every structure of UniProt P18434
- Elsewhere: RCSB PDB 2YN9 · PDBe 2YN9 · UniProt P19156 · UniProt P18434
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