Research workbench
Cryo-EM structure of the tavapadon-bound D1 dopamine receptor and mini-gs complex
Analyse Cryo-EM structure of the tavapadon-bound D1 dopamine receptor and mini-gs… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X2D
- Type
- protein
- Length
- 1,032 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, 86W
- Pockets
- 13 · 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 | 280 | 85% helix, 0% strand | P21728 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 229 | 48% helix, 16% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 47% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 57% helix, 0% strand | P59768 |
| E | NANOBODY35 | protein | 128 | 5% helix, 43% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains F
- 86W · 1,5-dimethyl-6-[2-methyl-4-[3-(trifluoromethyl)pyridin-2-yl]oxy-phenyl]pyrimidine-2,4-dione · ligand · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.83 | 0.86 | 81 | empty |
| 2 | 216 | 0.76 | 0.90 | 38 | 86W |
| 3 | 983 | 0.75 | 0.78 | 66 | empty |
| 4 | 867 | 0.73 | 0.78 | 59 | empty |
| 5 | 411 | 0.72 | 0.83 | 61 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2215 Ų buried · 13 hydrogen bonds · protein-protein
- F–A · 1548 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1429 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 833 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 571 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7X2D · Cryo-EM structure of the tavapadon-bound D1 dopamine receptor and mini-Gs complex · 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 0.94
- 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 0.91
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 7X2D · PDBe 7X2D · UniProt P21728 · UniProt P62873 · UniProt P59768
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