MolNFT v1 · #178009 · protein
Cryo-EM structure of the GDP-bound dopamine receptor 1 and mini-gs complex with NB35
7F1O · D(1A) dopamine receptor: “Cryo-EM structure of the GDP-bound dopamine receptor 1 and mini-gs complex with NB35”. Electron microscopy, 3 ligands (LDP, GDP, MG), 14 pockets (best druggability 0.83). MolNFT v1 #178009 on GenesisL1: 3D…
- PDB
- 7F1O
- Type
- protein
- Length
- 1,035 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
- LDP, GDP, MG
- Pockets
- 14 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | D(1A) dopamine receptor | protein | 277 | 85% helix, 1% 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 | 235 | 48% helix, 17% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 46% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 63% helix, 0% strand | P59768 |
| E | Nanobody 35 | protein | 128 | 5% helix, 40% strand | — |
Ligands and binding sites
- LDP · L-dopamine · ligand · chains F
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.83 | 0.84 | 104 | empty |
| 2 | 900 | 0.76 | 0.79 | 60 | empty |
| 3 | 918 | 0.74 | 0.78 | 65 | empty |
| 4 | 451 | 0.72 | 0.82 | 53 | empty |
| 5 | 316 | 0.71 | 0.84 | 38 | LDP |
Interfaces
6 interfaces between chains.
- B–D · 2285 Ų buried · 21 hydrogen bonds · protein-protein
- F–A · 1562 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1390 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 727 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 614 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7F1O · Cryo-EM structure of the GDP-bound dopamine receptor 1 and mini-Gs complex with Nb35 · the same entry in another collection · chain E against E, 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 1.00
- 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 0.93
- 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 P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7F1O · PDBe 7F1O · UniProt P21728 · UniProt P63092 · UniProt P62873 · UniProt P59768
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