MolNFT v1 · #154224 · protein

Cryo-EM structure of ALPHA2BAR-GI1 complex

6K42 · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Cryo-EM structure of ALPHA2BAR-GI1 complex”. Electron microscopy, 1 ligand (CZX), 15 pockets (best druggability 0.83). MolNFT v1 #154224 on GenesisL1: 3D structure, binding…

PDB: 6K42
Type: protein
Length: 1,116 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
EC: 3.2.1.17
UniProt: P63097, P62874, P59768, P08913, A0A097J809, P18089
Ligands: CZX
Pockets: 15 · best druggability 0.83

Structure

electron microscopy · 5 distinct chains · 29% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(I) subunit alpha-1	protein	218	35% helix, 14% strand	P63097
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	340	5% helix, 37% strand	P62874
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	55	53% helix, 0% strand	P59768
R	Alpha-2A adrenergic RECEPTOR,ENDOLYSIN,ALPHA-2B adrenergic RECEPTOR,ALPHA-2B adrenergic receptor (EC 3.2.1.17)	protein	270	76% helix, 0% strand	P08913, A0A097J809, P18089
H	Scfv	protein	233	0% helix, 39% strand	—

Ligands and binding sites

CZX · 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole · ligand · chains R

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 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	908	0.83	0.84	65	empty
2	1093	0.80	0.81	97	empty
3	116	0.77	0.96	29	empty
4	527	0.74	0.82	53	CZX
5	312	0.63	0.79	47	empty

Interfaces

6 interfaces between chains.

B–G · 1980 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 1296 Å² buried · 12 hydrogen bonds · protein-protein
A–R · 1112 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 559 Å² buried · 2 hydrogen bonds · protein-protein
B–H · 516 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6K42 · cryo-EM structure of alpha2BAR-Gi1 complex · the same entry in another collection · chain H against H, TM-score 1.00
P62874 · 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 0.98
P18089 · AlphaFold monomer V2.0 prediction for alpha-2B adrenergic receptor (P18089) · a predicted model of the same protein · chain R against A, TM-score 0.91
P08913 · AlphaFold monomer V2.0 prediction for alpha-2A adrenergic receptor (P08913) · a predicted model of the same protein · chain R against A, TM-score 0.90
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
P63097 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.78

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 P63097
Every structure of UniProt P62874
Every structure of UniProt P59768
Every structure of UniProt P08913
Every structure of UniProt A0A097J809
Every structure of UniProt P18089
Elsewhere: RCSB PDB 6K42 · PDBe 6K42 · UniProt P63097 · UniProt P62874 · UniProt P59768 · UniProt P08913 · UniProt A0A097J809 · UniProt P18089

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