Research workbench
Structure of pancreatic ATP-sensitive potassium channel bound with glibenclamide and atpgammas (CLASS2 at 4.57A)
Analyse Structure of pancreatic ATP-sensitive potassium channel bound with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YKG
- Type
- protein
- Length
- 6,536 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-sensitive inward rectifier potassium channel 11; ATP-binding cassette sub-family C…
- UniProt
- Q61743, A0A1U7R319
- Ligands
- AGS, GBM
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | ATP-sensitive inward rectifier potassium channel 11 | protein | 325 | 28% helix, 22% strand | Q61743 |
| B, D, F, H | ATP-binding cassette sub-family C member 8 isoform X2 | protein | 1309 | 66% helix, 7% strand | A0A1U7R319 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 8 copies · chains A, G, B, C, D, E, F, H
- GBM · 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl) sulfamoyl]phenyl}ethyl)-2-methoxybenzamide · ligand · 4 copies · chains B, D, F, H
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 | 567 | 0.85 | 0.91 | 51 | empty |
| 2 | 687 | 0.83 | 0.87 | 82 | GBM |
| 3 | 851 | 0.83 | 0.85 | 103 | GBM |
| 4 | 818 | 0.83 | 0.85 | 99 | empty |
| 5 | 668 | 0.82 | 0.86 | 84 | GBM |
Interfaces
14 interfaces between chains.
- E–G · 2766 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 2764 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 2762 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 2761 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1014 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5YKG · Structure of pancreatic ATP-sensitive potassium channel bound with glibenclamide and… · the same entry in another collection · chain H against H, TM-score 1.00
- Q61743 · AlphaFold monomer V2.0 prediction for ATP-sensitive inward rectifier potassium channel 11… · a predicted model of the same protein · chain A against A, TM-score 0.85
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 Q61743
- Every structure of UniProt A0A1U7R319
- Elsewhere: RCSB PDB 5YKG · PDBe 5YKG · UniProt Q61743 · UniProt A0A1U7R319
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