MolNFT v1 · #154223 · protein

Cryo-EM structure of ALPHA2BAR-goa complex

6K41 · Guanine nucleotide-binding protein G(O) subunit alpha: “Cryo-EM structure of ALPHA2BAR-goa complex”. Electron microscopy, 1 ligand (CZX), 9 pockets (best druggability 0.83). MolNFT v1 #154223 on GenesisL1: 3D structure, binding…

PDB: 6K41
Type: protein
Length: 1,077 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(O) subunit alpha; Guanine nucleotide-binding protein…
EC: 3.2.1.17
UniProt: P09471, P62874, P59768, Q28838, A0A097J809, P18089
Ligands: CZX
Pockets: 9 · best druggability 0.83

Structure

electron microscopy · 5 distinct chains · 33% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(O) subunit alpha	protein	213	44% helix, 17% strand	P09471
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	333	6% helix, 48% strand	P62874
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	55	58% helix, 0% strand	P59768
R	Alpha-2A adrenergic RECEPTOR,ENDOLYSIN,ALPHA-2B adrenergic RECEPTOR,ALPHA-2B adrenergic receptor (EC 3.2.1.17)	protein	243	82% helix, 0% strand	Q28838, A0A097J809, P18089
H	Scfv	protein	233	3% helix, 48% 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

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	916	0.83	0.85	68	empty
2	1155	0.81	0.82	107	empty
3	214	0.72	0.88	36	CZX
4	513	0.67	0.78	68	empty
5	109	0.53	0.83	25	empty

Interfaces

6 interfaces between chains.

B–G · 2074 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1191 Å² buried · 16 hydrogen bonds · protein-protein
A–R · 995 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 540 Å² buried · 6 hydrogen bonds · protein-protein
B–H · 459 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6K41 · cryo-EM structure of alpha2BAR-GoA 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 1.00
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 0.93
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 0.92
Q28838 · AlphaFold monomer V2.0 prediction for alpha-2A adrenergic receptor (Q28838) · a predicted model of the same protein · chain R against A, TM-score 0.91
P09471 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(O) 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 P09471
Every structure of UniProt P62874
Every structure of UniProt P59768
Every structure of UniProt Q28838
Every structure of UniProt A0A097J809
Every structure of UniProt P18089
Elsewhere: RCSB PDB 6K41 · PDBe 6K41 · UniProt P09471 · UniProt P62874 · UniProt P59768 · UniProt Q28838 · UniProt A0A097J809 · UniProt P18089

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