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Cryo-EM structure of cyanopindolol-bound BETA1-adrenergic receptor in complex with heterotrimeric gs-protein

Analyse Cryo-EM structure of cyanopindolol-bound BETA1-adrenergic receptor in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8DCS
Type: protein
Length: 1,000 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1; Nanobody 35; Guanine…
EC: 3.2.1.17
UniProt: P62871, P04896, P63212, P00720
Ligands: P32
Pockets: 14 · best druggability 0.82

Structure

electron microscopy · 5 distinct chains · 39% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	338	8% helix, 47% strand	P62871
N	Nanobody 35	protein	130	7% helix, 43% strand	—
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	200	49% helix, 20% strand	P04896
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	57	53% helix, 0% strand	P63212
R	ENDOLYSIN,ENDOLYSIN,BETA-1 adrenergic receptor chimera (EC 3.2.1.17)	protein	275	82% helix, 1% strand	P00720

Ligands and binding sites

P32 · 4-{[(2S)-3-(tert-butylamino)-2-hydroxypropyl]oxy}-3H-indole-2-carbonitrile · ligand · chains R

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

Pockets

14 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	761	0.82	0.85	59	empty
2	975	0.76	0.79	70	empty
3	370	0.76	0.86	40	P32
4	397	0.70	0.82	58	empty
5	181	0.68	0.87	27	empty

Interfaces

6 interfaces between chains.

B–G · 2165 Å² buried · 13 hydrogen bonds · protein-protein
B–A · 1496 Å² buried · 27 hydrogen bonds · protein-protein
A–R · 1109 Å² buried · 8 hydrogen bonds · protein-protein
N–A · 962 Å² buried · 11 hydrogen bonds · protein-protein
B–N · 543 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

8DCS · Cryo-EM structure of cyanopindolol-bound beta1-adrenergic receptor in complex with… · the same entry in another collection · chain R against R, TM-score 1.00
P62871 · 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
P04896 · 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 0.82
P63212 · 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 0.62

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 P62871
Every structure of UniProt P04896
Every structure of UniProt P63212
Every structure of UniProt P00720
Elsewhere: RCSB PDB 8DCS · PDBe 8DCS · UniProt P62871 · UniProt P04896 · UniProt P63212 · UniProt P00720

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