Research workbench
Cryo-EM structure of apomorphine-bound dopamine receptor 1 in complex with gs protein
Analyse Cryo-EM structure of apomorphine-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
- 7JVQ
- Type
- protein
- Length
- 1,047 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D(1A) dopamine receptor; Engineered mini-gi protein alpha sub-unit; Guanine…
- UniProt
- P21728, P62873, P59768
- Ligands
- CLR, PLM, OR9
- Pockets
- 16 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | D(1A) dopamine receptor | protein | 286 | 83% helix, 0% strand | P21728 |
| A | Engineered mini-gi protein alpha sub-unit | protein | 238 | 45% helix, 18% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 44% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 54% helix, 0% strand | P59768 |
| N | NANOBODY35 | protein | 128 | 5% helix, 46% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 5 copies · chains R
- PLM · Palmitic acid · ligand · 3 copies · chains R
- OR9 · (6AR)-6-methyl-5,6,6A,7-tetrahydro-4H-dibenzo[de, g]quinoline-10,11-diol · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.84 | 0.86 | 75 | empty |
| 2 | 411 | 0.77 | 0.86 | 41 | OR9 |
| 3 | 846 | 0.75 | 0.79 | 67 | empty |
| 4 | 882 | 0.75 | 0.78 | 64 | empty |
| 5 | 307 | 0.66 | 0.82 | 41 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2129 Ų buried · 12 hydrogen bonds · protein-protein
- R–A · 1658 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1576 Ų buried · 17 hydrogen bonds · protein-protein
- A–N · 876 Ų buried · 4 hydrogen bonds · protein-protein
- B–N · 648 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7JVQ · Cryo-EM structure of apomorphine-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 P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7JVQ · PDBe 7JVQ · UniProt P21728 · UniProt P62873 · UniProt P59768
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