MolNFT v1 · #146298 · protein
Mu opioid receptor-gi protein complex
6DDE · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Mu opioid receptor-gi protein complex”. Electron microscopy, 1 ligand (ETA), 9 pockets (best druggability 0.81). MolNFT v1 #146298 on GenesisL1: 3D structure, binding sites…
- PDB
- 6DDE
- Type
- protein
- Length
- 1,123 residues
- Chains
- 6
- 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, P42866
- Ligands
- ETA
- Pockets
- 9 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 217 | 41% helix, 16% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 6% helix, 42% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 43% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 232 | 3% helix, 48% strand | — |
| R | Mu-type opioid receptor | protein | 281 | 74% helix, 0% strand | P42866 |
| D | Damgo | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ETA · Ethanolamine · ligand · chains R, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.81 | 0.86 | 59 | empty |
| 2 | 850 | 0.70 | 0.76 | 66 | empty |
| 3 | 282 | 0.60 | 0.78 | 41 | ETA |
| 4 | 255 | 0.59 | 0.79 | 50 | empty |
| 5 | 92 | 0.51 | 0.82 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2023 Ų buried · 10 hydrogen bonds · protein-protein
- A–R · 1267 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1254 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 575 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 500 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent, 1 d-amino, 1 modified (disulfide, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 6DDE · Mu Opioid Receptor-Gi Protein Complex · the same entry in another collection · chain D against D, 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
- P42866 · AlphaFold monomer V2.0 prediction for mu-type opioid receptor (P42866) · a predicted model of the same protein · chain R against A, TM-score 0.95
- 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 0.82
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 P42866
- Elsewhere: RCSB PDB 6DDE · PDBe 6DDE · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P42866
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