MolNFT v1 · #175317 · protein
Dopamine receptor D3R-gi-PD128907 complex
7CMV · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Dopamine receptor D3R-gi-PD128907 complex”. Electron microscopy, 1 ligand (G6O), 10 pockets (best druggability 0.82). MolNFT v1 #175317 on GenesisL1: 3D structure, binding…
- PDB
- 7CMV
- 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
- G6O
- Pockets
- 10 · best druggability 0.82
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 | 51% helix, 18% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 337 | 7% helix, 48% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 52% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 231 | 5% helix, 48% strand | — |
| R | Soluble cytochrome B562,D(3) dopamine receptor | protein | 272 | 83% helix, 0% strand | P35462 |
Ligands and binding sites
- G6O · (4aR,10bR)-4-propyl-3,4a,5,10b-tetrahydro-2H-chromeno[4,3-b][1,4]oxazin-9-ol · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.82 | 0.84 | 66 | empty |
| 2 | 405 | 0.74 | 0.84 | 40 | G6O |
| 3 | 959 | 0.72 | 0.76 | 79 | empty |
| 4 | 169 | 0.61 | 0.84 | 25 | empty |
| 5 | 294 | 0.60 | 0.78 | 41 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2272 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1187 Ų buried · 15 hydrogen bonds · protein-protein
- A–R · 1137 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 590 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 427 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7CMV · Dopamine Receptor D3R-Gi-PD128907 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 0.92
- 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 0.82
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 7CMV · PDBe 7CMV · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P35462
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