MolNFT v1 · #178891 · protein

Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist

7JOZ · Guanine nucleotide-binding protein G(S) subunit alpha…: “Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist”. X-ray diffraction, 1 ligand (VFP), 17 pockets (best druggability 0.84). MolNFT…

PDB: 7JOZ
Type: protein
Length: 1,309 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
EC: 3.2.1.17
UniProt: P63092, P62873, P59768, D9IEF7, P21728
Ligands: VFP
Pockets: 17 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 38% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	338	43% helix, 12% strand	P63092
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	340	6% helix, 41% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	57	37% helix, 0% strand	P59768
N	Nanobody 35	protein	128	2% helix, 40% strand	—
R	ENDOLYSIN,D(1A) dopamine receptor (EC 3.2.1.17)	protein	446	69% helix, 2% strand	D9IEF7, P21728

Ligands and binding sites

VFP · 6-{4-[(furo[3,2-c]pyridin-4-yl)oxy]-2-methylphenyl}-1, 5-dimethylpyrimidine-2,4(1H,3H)-dione · ligand · chains R
1PE · Pentaethylene glycol · additive · chains R

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

Pockets

17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1013	0.84	0.85	81	empty
2	922	0.80	0.82	83	VFP
3	294	0.73	0.86	29	empty
4	1171	0.72	0.76	97	empty
5	934	0.71	0.75	65	empty

Interfaces

6 interfaces between chains.

B–G · 1837 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1800 Å² buried · 17 hydrogen bonds · protein-protein
A–R · 1556 Å² buried · 9 hydrogen bonds · protein-protein
A–N · 861 Å² buried · 5 hydrogen bonds · protein-protein
B–N · 410 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7JOZ · Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol… · 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 0.97
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 0.82
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 0.61

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 D9IEF7
Every structure of UniProt P21728
Elsewhere: RCSB PDB 7JOZ · PDBe 7JOZ · UniProt P63092 · UniProt P62873 · UniProt P59768 · UniProt D9IEF7 · UniProt P21728

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