MolNFT v1 · #188642 · protein
Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and glibenclamide with KIR6.2-ctd in the up conformation
7U24 · ATP-sensitive inward rectifier potassium channel 11: “Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and glibenclamide with…”. Electron microscopy, 6 ligands (P5S, ATP, PTY), 20 pockets (best…
- PDB
- 7U24
- Type
- protein
- Length
- 2,770 residues
- Chains
- 5
- 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
- P70673, Q09427
- Ligands
- P5S, ATP, PTY, POV, GBM, NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-sensitive inward rectifier potassium channel 11 | protein | 359 | 31% helix, 20% strand | P70673 |
| B, C, D | ATP-sensitive inward rectifier potassium channel 11 | protein | 328 | 32% helix, 24% strand | P70673 |
| E | ATP-binding cassette sub-family C member 8 | protein | 1427 | 63% helix, 5% strand | Q09427 |
Ligands and binding sites
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · 9 copies · chains A, D, B, E, C
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains A, D, B, E, C
- PTY · Phosphatidylethanolamine · ligand · 5 copies · chains A, E
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 4 copies · chains A, D, E, B, C
- GBM · 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl) sulfamoyl]phenyl}ethyl)-2-methoxybenzamide · ligand · chains A, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
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 | 1069 | 0.89 | 0.91 | 127 | GBM |
| 2 | 1007 | 0.88 | 0.90 | 118 | empty |
| 3 | 548 | 0.87 | 0.92 | 50 | empty |
| 4 | 971 | 0.82 | 0.83 | 122 | empty |
| 5 | 486 | 0.81 | 0.88 | 77 | empty |
Interfaces
8 interfaces between chains.
- B–C · 3349 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 3279 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 3273 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 3227 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 2490 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- P70673 · AlphaFold monomer V2.0 prediction for ATP-sensitive inward rectifier potassium channel 11… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q09427 · AlphaFold monomer V2.0 prediction for ATP-binding cassette sub-family C member 8 (Q09427) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P70673
- Every structure of UniProt Q09427
- Elsewhere: RCSB PDB 7U24 · PDBe 7U24 · UniProt P70673 · UniProt Q09427
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