MolNFT v1 · #179114 · protein
Cryo-EM structure of skf-83959-bound dopamine receptor 1 in complex with gs protein
7JVP · D(1A) dopamine receptor: “Cryo-EM structure of skf-83959-bound dopamine receptor 1 in complex with gs protein”. Electron microscopy, 3 ligands (CLR, PLM, SK9), 17 pockets (best druggability 0.80). MolNFT v1 #179114 on GenesisL1: 3D…
- PDB
- 7JVP
- Type
- protein
- Length
- 1,041 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, SK9
- Pockets
- 17 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | D(1A) dopamine receptor | protein | 280 | 86% helix, 1% strand | P21728 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 237 | 52% helix, 17% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 9% helix, 48% 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, 45% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 6 copies · chains R
- PLM · Palmitic acid · ligand · 5 copies · chains R
- SK9 · (1R)-6-chloro-3-methyl-1-(3-methylphenyl)-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
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.80 | 0.87 | 58 | empty |
| 2 | 763 | 0.78 | 0.82 | 55 | empty |
| 3 | 1174 | 0.77 | 0.79 | 65 | empty |
| 4 | 313 | 0.76 | 0.87 | 33 | SK9 |
| 5 | 149 | 0.68 | 0.89 | 24 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2248 Ų buried · 15 hydrogen bonds · protein-protein
- R–A · 1659 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1562 Ų buried · 22 hydrogen bonds · protein-protein
- A–N · 1088 Ų buried · 11 hydrogen bonds · protein-protein
- B–N · 706 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7JVP · Cryo-EM structure of SKF-83959-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 0.92
- 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 0.90
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 P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7JVP · PDBe 7JVP · UniProt P21728 · UniProt P63092 · UniProt P62873 · UniProt P59768
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