Research workbench

B2V2R-Gs protein subcomplex of a GPCR-G protein-beta-arrestin mega-complex

Analyse B2V2R-Gs protein subcomplex of a GPCR-G protein-beta-arrestin mega-complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NI3
Type: protein
Length: 1,043 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.8
Source: Enterobacteria phage RB59; Homo sapiens; Lama glama
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 · resolution 3.8 · 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.

Pocket	Volume (Å³)	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 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1594 Å² buried · 18 hydrogen bonds · protein-protein
A–R · 1386 Å² buried · 10 hydrogen bonds · protein-protein
A–N · 926 Å² buried · 6 hydrogen bonds · protein-protein
B–N · 667 Å² 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 R against R, 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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