MolNFT v1 · #169525 · protein
Cryoem structure of GIRK2-PIP2/CHS - G protein-gated inwardly rectifying potassium channel GIRK2 with modulators cholesteryl hemisuccinate and PIP2
6XEV · G protein-activated inward rectifier potassium channel 2: “Cryoem structure of GIRK2-PIP2/CHS - G protein-gated inwardly rectifying potassium channel GIRK2 with…”. Electron microscopy, 4 ligands (PIO, Y01, K), 20 pockets (best…
- PDB
- 6XEV
- Type
- protein
- Length
- 1,312 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G protein-activated inward rectifier potassium channel 2
- UniProt
- A0A338P6L0
- Ligands
- PIO, Y01, K, NA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | G protein-activated inward rectifier potassium channel 2 | protein | 328 | 31% helix, 23% strand | A0A338P6L0 |
Ligands and binding sites
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 4 copies · chains A, E, I, M
- Y01 · Cholesterol hemisuccinate · ligand · 4 copies · chains A, M, E, I
- K · Potassium ion · metal · 13 copies · chains A, E, I, M
- NA · Sodium ion · metal · 4 copies · chains A, E, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.86 | 0.87 | 113 | K |
| 2 | 755 | 0.79 | 0.83 | 50 | K |
| 3 | 628 | 0.74 | 0.81 | 74 | empty |
| 4 | 529 | 0.73 | 0.81 | 51 | empty |
| 5 | 482 | 0.73 | 0.82 | 53 | empty |
Interfaces
6 interfaces between chains.
- I–M · 3166 Ų buried · 16 hydrogen bonds · protein-protein
- A–M · 3162 Ų buried · 16 hydrogen bonds · protein-protein
- E–I · 3160 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 3159 Ų buried · 16 hydrogen bonds · protein-protein
- E–M · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6XEV · CryoEM structure of GIRK2-PIP2/CHS - G protein-gated inwardly rectifying potassium… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A338P6L0
- Elsewhere: RCSB PDB 6XEV · PDBe 6XEV · UniProt A0A338P6L0
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