Research workbench
Structure of a D2 dopamine receptor-G-protein complex in a lipid membrane
Analyse Structure of a D2 dopamine receptor-G-protein complex in a lipid membrane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VMS
- Type
- protein
- Length
- 1,135 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- EC
- 3.2.1.17
- UniProt
- P10824, P62873, P59768, D9IEF7, P14416
- Ligands
- 08Y
- Pockets
- 14 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 227 | 44% helix, 18% strand | P10824 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 49% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 59 | 54% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 232 | 5% helix, 49% strand | — |
| R | ENDOLYSIN,D(2) dopamine RECEPTOR,D(2) dopamine receptor (EC 3.2.1.17) | protein | 278 | 78% helix, 0% strand | D9IEF7, P14416 |
Ligands and binding sites
- 08Y · bromoergocryptine · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.81 | 0.85 | 67 | empty |
| 2 | 1034 | 0.78 | 0.80 | 81 | empty |
| 3 | 534 | 0.76 | 0.83 | 43 | 08Y |
| 4 | 314 | 0.64 | 0.80 | 34 | empty |
| 5 | 311 | 0.62 | 0.79 | 47 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2221 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1248 Ų buried · 10 hydrogen bonds · protein-protein
- A–R · 1141 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 561 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 403 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6VMS · Structure of a D2 dopamine receptor-G-protein complex in a lipid membrane · the same entry in another collection · chain R against R, 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 C against A, TM-score 0.92
- P14416 · AlphaFold monomer V2.0 prediction for D(2) dopamine receptor (P14416) · a predicted model of the same protein · chain R against A, TM-score 0.88
- P10824 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.81
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 P10824
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt D9IEF7
- Every structure of UniProt P14416
- Elsewhere: RCSB PDB 6VMS · PDBe 6VMS · UniProt P10824 · UniProt P62873 · UniProt P59768 · UniProt D9IEF7 · UniProt P14416
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