MolNFT v1 · #97490 · protein
Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (KIR3.2) in complex with the beta-gamma G protein subunits
4KFM · G protein-activated inward rectifier potassium channel 2: “Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (KIR3.2) in complex with the…”. X-ray diffraction, 3 ligands (PIO, K, NA), 6 pockets (best…
- PDB
- 4KFM
- Type
- protein
- Length
- 727 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G protein-activated inward rectifier potassium channel 2; Guanine nucleotide-binding…
- UniProt
- Q8C4T8, P62873, P59768
- Ligands
- PIO, K, NA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G protein-activated inward rectifier potassium channel 2 | protein | 328 | 35% helix, 27% strand | Q8C4T8 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 48% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 60 | 55% helix, 0% strand | P59768 |
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 · chains A
- K · Potassium ion · metal · 5 copies · chains A
- NA · Sodium ion · metal · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.79 | 0.83 | 64 | empty |
| 2 | 392 | 0.59 | 0.75 | 35 | empty |
| 3 | 225 | 0.51 | 0.76 | 36 | empty |
| 4 | 52 | 0.36 | 0.79 | 14 | empty |
| 5 | 87 | 0.33 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–G · 2318 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 275 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4KFM · Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in… · the same entry in another collection · chain A against A, TM-score 1.00
- P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.84
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 Q8C4T8
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 4KFM · PDBe 4KFM · UniProt Q8C4T8 · UniProt P62873 · UniProt P59768
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