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Cryo-EM structure of skf-81297-bound dopamine receptor 1 in complex with gs protein

Analyse Cryo-EM structure of skf-81297-bound dopamine receptor 1 in complex with gs… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JV5
Type: protein
Length: 1,044 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D(1A) dopamine receptor; Guanine nucleotide-binding protein G(S) subunit alpha isoforms…
UniProt: P21728, P63092, P62873, P59768
Ligands: CLR, PLM, SK0
Pockets: 15 · best druggability 0.84

Structure

electron microscopy · 5 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	D(1A) dopamine receptor	protein	282	84% helix, 0% strand	P21728
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	238	48% helix, 17% strand	P63092
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	9% helix, 43% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	57	54% helix, 0% strand	P59768
N	Nanobody 35	protein	128	2% helix, 43% strand	—

Ligands and binding sites

CLR · Cholesterol · ligand · 6 copies · chains R
PLM · Palmitic acid · ligand · 6 copies · chains R
SK0 · (1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol · 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	893	0.84	0.86	78	empty
2	360	0.77	0.87	38	SK0
3	1011	0.76	0.78	72	empty
4	405	0.74	0.85	71	empty
5	799	0.74	0.79	60	empty

Interfaces

7 interfaces between chains.

B–G · 2102 Å² buried · 10 hydrogen bonds · protein-protein
R–A · 1617 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1582 Å² buried · 19 hydrogen bonds · protein-protein
A–N · 1075 Å² buried · 8 hydrogen bonds · protein-protein
B–N · 631 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7JV5 · Cryo-EM structure of SKF-81297-bound dopamine receptor 1 in complex with Gs protein · 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
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 0.93
P21728 · AlphaFold monomer V2.0 prediction for D(1A) dopamine receptor (P21728) · a predicted model of the same protein · chain R against A, TM-score 0.89

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 P21728
Every structure of UniProt P63092
Every structure of UniProt P62873
Every structure of UniProt P59768
Elsewhere: RCSB PDB 7JV5 · PDBe 7JV5 · UniProt P21728 · UniProt P63092 · UniProt P62873 · UniProt P59768

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