Research workbench
Crystal structure of the gastric proton pump complexed with soraprazan
Analyse Crystal structure of the gastric proton pump complexed with soraprazan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W49
- Type
- protein
- Length
- 1,247 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
- 3.6.3.10
- UniProt
- P19156, P18434
- Ligands
- 8CE, NAG, RB, MG
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium-transporting ATPase alpha chain 1 (EC 3.6.3.10) | protein | 987 | 47% helix, 15% strand | P19156 |
| B | Potassium-transporting ATPase subunit beta | protein | 260 | 22% helix, 22% strand | P18434 |
Ligands and binding sites
- 8CE · Soraprazan · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
- RB · Rubidium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.76 | 0.82 | 52 | 8CE |
| 2 | 801 | 0.73 | 0.79 | 69 | empty |
| 3 | 447 | 0.73 | 0.82 | 42 | empty |
| 4 | 90 | 0.64 | 0.90 | 22 | empty |
| 5 | 230 | 0.59 | 0.80 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2074 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 7W49 · Crystal structure of the gastric proton pump complexed with soraprazan · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.96
- 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 0.93
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 7W49 · PDBe 7W49 · UniProt P19156 · UniProt P18434
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