Research workbench
Allosteric modulator LY3154207 binding to dopamine-bound dopamine receptor 1 in complex with minigs protein
Analyse Allosteric modulator LY3154207 binding to dopamine-bound dopamine receptor 1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LJD
- Type
- protein
- Length
- 1,046 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D(1A) dopamine receptor; Engineered gs protein alpha subunit; Guanine nucleotide-binding…
- UniProt
- P21728, P54311, P63212
- Ligands
- CLR, PLM, LDP, G4C
- Pockets
- 15 · 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 | 285 | 84% helix, 0% strand | P21728 |
| A | Engineered gs protein alpha subunit | protein | 238 | 45% helix, 17% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 46% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 53% helix, 0% strand | P63212 |
| N | Nanobody 35 | protein | 128 | 2% helix, 45% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 5 copies · chains R
- PLM · Palmitic acid · ligand · 4 copies · chains R
- LDP · L-dopamine · ligand · chains R
- 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 R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.84 | 0.87 | 75 | empty |
| 2 | 1197 | 0.78 | 0.80 | 92 | empty |
| 3 | 844 | 0.76 | 0.80 | 64 | empty |
| 4 | 402 | 0.74 | 0.84 | 41 | LDP |
| 5 | 514 | 0.72 | 0.81 | 65 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2141 Ų buried · 9 hydrogen bonds · protein-protein
- R–A · 1799 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1586 Ų buried · 21 hydrogen bonds · protein-protein
- A–N · 951 Ų buried · 5 hydrogen bonds · protein-protein
- B–N · 661 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7LJD · Allosteric modulator LY3154207 binding to dopamine-bound dopamine receptor 1 in complex… · the same entry in another collection · chain N against N, TM-score 1.00
- P54311 · 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
- 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
- P63212 · 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 0.67
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 P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7LJD · PDBe 7LJD · UniProt P21728 · UniProt P54311 · UniProt P63212
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