Research workbench
Rb+-bound E2-alf state of the gastric proton pump (TYR799TRP)
Analyse Rb+-bound E2-alf state of the gastric proton pump (TYR799TRP) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JXJ
- Type
- protein
- Length
- 1,249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium-transporting ATPase alpha chain 1; Potassium-transporting ATPase subunit beta
- EC
- 7.2.2.19
- UniProt
- P19156, P18434
- Ligands
- PCW, CE1, ALF, CLR, NAG, RB, MG
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium-transporting ATPase alpha chain 1 (EC 7.2.2.19) | protein | 987 | 50% helix, 16% strand | P19156 |
| B | Potassium-transporting ATPase subunit beta | protein | 262 | 23% helix, 23% strand | P18434 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, B
- CE1 · O-dodecanyl octaethylene glycol · ligand · chains A
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- CLR · Cholesterol · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B
- RB · Rubidium ion · metal · 8 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.77 | 0.81 | 60 | RB |
| 2 | 794 | 0.74 | 0.78 | 64 | empty |
| 3 | 334 | 0.66 | 0.81 | 40 | empty |
| 4 | 79 | 0.60 | 0.89 | 21 | empty |
| 5 | 281 | 0.56 | 0.77 | 41 | RB |
Interfaces
1 interface between chains.
- A–B · 2219 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 6JXJ · Rb+-bound E2-AlF state of the gastric proton pump (Tyr799Trp) · 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 0.99
- 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 0.95
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 6JXJ · PDBe 6JXJ · UniProt P19156 · UniProt P18434
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