Research workbench
Structure of pancreatic ATP-sensitive potassium channel bound with repaglinide and atpgammas at 3.3A resolution
Analyse Structure of pancreatic ATP-sensitive potassium channel bound with repaglinide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JB1
- Type
- protein
- Length
- 6,772 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
- POV, PTY, AGS, AJP, BJX
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | ATP-sensitive inward rectifier potassium channel 11 | protein | 327 | 29% helix, 25% strand | Q61743 |
| B, D, F, H | ATP-binding cassette sub-family C member 8 isoform X2 | protein | 1366 | 64% helix, 7% strand | A0A1U7R319 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 36 copies · chains A, B, C, D, E, F, G, H
- PTY · Phosphatidylethanolamine · ligand · 16 copies · chains B, D, F, H
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 8 copies · chains A, B, G, C, D, E, F, H
- AJP · Digitonin · ligand · 4 copies · chains B, D, F, H
- BJX · Repaglinide · 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 | 1019 | 0.87 | 0.88 | 99 | empty |
| 2 | 525 | 0.85 | 0.91 | 58 | empty |
| 3 | 1008 | 0.84 | 0.85 | 114 | AJP, BJX |
| 4 | 989 | 0.84 | 0.85 | 111 | AJP, BJX |
| 5 | 1039 | 0.83 | 0.84 | 107 | AJP, BJX |
Interfaces
14 interfaces between chains.
- A–G · 3329 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 3325 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 3319 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 3317 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1575 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6JB1 · Structure of pancreatic ATP-sensitive potassium channel bound with repaglinide 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 0.96
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 Q61743
- Every structure of UniProt A0A1U7R319
- Elsewhere: RCSB PDB 6JB1 · PDBe 6JB1 · UniProt Q61743 · UniProt A0A1U7R319
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