MolNFT v1 · #158034 · protein
B2V2R-gs protein subcomplex of a GPCR-G protein-beta-arrestin mega- complex
6NI3 · Guanine nucleotide-binding protein G(S) subunit alpha…: “B2V2R-gs protein subcomplex of a GPCR-G protein-beta-arrestin mega- complex”. Electron microscopy, 1 ligand (P0G), 16 pockets (best druggability 0.80). MolNFT v1 #158034 on…
- PDB
- 6NI3
- Type
- protein
- Length
- 1,043 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
- EC
- 3.2.1.17
- UniProt
- P63092, P62873, P59768, A0A097J809, P07550
- Ligands
- P0G
- Pockets
- 16 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 234 | 46% helix, 17% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 45% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 60% helix, 0% strand | P59768 |
| R | ENDOLYSIN,BETA-2 adrenergic receptor chimera (EC 3.2.1.17) | protein | 284 | 84% helix, 0% strand | A0A097J809, P07550 |
| N | Nanobody 35 | protein | 128 | 5% helix, 45% strand | — |
Ligands and binding sites
- P0G · 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl) ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.80 | 0.85 | 55 | empty |
| 2 | 482 | 0.80 | 0.87 | 61 | P0G |
| 3 | 953 | 0.77 | 0.80 | 64 | empty |
| 4 | 951 | 0.77 | 0.79 | 84 | empty |
| 5 | 139 | 0.74 | 0.93 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2197 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1594 Ų buried · 18 hydrogen bonds · protein-protein
- A–R · 1386 Ų buried · 10 hydrogen bonds · protein-protein
- A–N · 926 Ų buried · 6 hydrogen bonds · protein-protein
- B–N · 667 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6NI3 · B2V2R-Gs protein subcomplex of a GPCR-G protein-beta-arrestin mega-complex · the same entry in another collection · chain N against N, 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
- P07550 · AlphaFold monomer V2.0 prediction for beta-2 adrenergic receptor (P07550) · a predicted model of the same protein · chain R against A, TM-score 0.93
- 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 0.86
- P63092 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain A 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 P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt A0A097J809
- Every structure of UniProt P07550
- Elsewhere: RCSB PDB 6NI3 · PDBe 6NI3 · UniProt P63092 · UniProt P62873 · UniProt P59768 · UniProt A0A097J809 · UniProt P07550
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