Research workbench
Dopamine receptor D3R-gi-pramipexole complex
Analyse Dopamine receptor D3R-gi-pramipexole complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CMU
- Type
- protein
- Length
- 1,123 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…
- UniProt
- P63096, P62873, P59768, P35462
- Ligands
- G6L
- Pockets
- 14 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 225 | 47% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 337 | 7% helix, 49% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 57% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 231 | 5% helix, 48% strand | — |
| R | Soluble cytochrome B562,D(3) dopamine receptor | protein | 272 | 84% helix, 0% strand | P35462 |
Ligands and binding sites
- G6L · (6S)-N6-propyl-4,5,6,7-tetrahydro-1,3-benzothiazole-2, 6-diamine · 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 | 852 | 0.83 | 0.85 | 67 | empty |
| 2 | 1064 | 0.73 | 0.76 | 94 | empty |
| 3 | 409 | 0.72 | 0.83 | 37 | G6L |
| 4 | 64 | 0.67 | 0.94 | 19 | empty |
| 5 | 312 | 0.63 | 0.80 | 45 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2214 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1174 Ų buried · 13 hydrogen bonds · protein-protein
- A–R · 1082 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 590 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 457 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7CMU · Dopamine Receptor D3R-Gi-Pramipexole complex · 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
- P35462 · AlphaFold monomer V2.0 prediction for D(3) dopamine receptor (P35462) · a predicted model of the same protein · chain R against A, TM-score 0.93
- 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 0.90
- P63096 · 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 P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P35462
- Elsewhere: RCSB PDB 7CMU · PDBe 7CMU · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P35462
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