MolNFT v1 · #190416 · protein
Cryo-EM structure of the dopamine and LY3154207-bound D1 dopamine receptor and mini-gs complex
7X2F · D(1A) dopamine receptor: “Cryo-EM structure of the dopamine and LY3154207-bound D1 dopamine receptor and mini-gs complex”. Electron microscopy, 3 ligands (CLR, G4C, LDP), 12 pockets (best druggability 0.84). MolNFT v1 #190416 on…
- PDB
- 7X2F
- Type
- protein
- Length
- 1,036 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, P62873, P59768
- Ligands
- CLR, G4C, LDP
- Pockets
- 12 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | D(1A) dopamine receptor | protein | 282 | 85% helix, 0% strand | P21728 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short, isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 228 | 49% helix, 17% strand | — |
| E | NANOBODY35 | protein | 128 | 5% helix, 43% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 341 | 9% helix, 47% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 56% helix, 0% strand | P59768 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains F
- G4C · 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone · ligand · chains F
- LDP · L-dopamine · ligand · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.84 | 0.87 | 76 | empty |
| 2 | 996 | 0.75 | 0.78 | 79 | empty |
| 3 | 920 | 0.73 | 0.77 | 67 | empty |
| 4 | 360 | 0.70 | 0.83 | 56 | empty |
| 5 | 265 | 0.68 | 0.83 | 36 | LDP |
Interfaces
7 interfaces between chains.
- B–D · 2159 Ų buried · 14 hydrogen bonds · protein-protein
- F–A · 1645 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1388 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 789 Ų buried · 8 hydrogen bonds · protein-protein
- E–B · 543 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7X2F · Cryo-EM structure of the dopamine and LY3154207-bound D1 dopamine receptor and mini-Gs… · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.90
- P21728 · AlphaFold monomer V2.0 prediction for D(1A) dopamine receptor (P21728) · a predicted model of the same protein · chain F against A, TM-score 0.90
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 P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7X2F · PDBe 7X2F · UniProt P21728 · UniProt P62873 · UniProt P59768
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.