Research workbench
Mu opioid receptor-gi protein complex
Analyse Mu opioid receptor-gi protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DDF
- Type
- protein
- Length
- 891 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, P42866
- Ligands
- ETA
- Pockets
- 6 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 217 | 39% helix, 14% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 6% helix, 43% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 38% helix, 0% strand | P59768 |
| R | Mu-type opioid receptor | protein | 281 | 71% 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.82 | 0.86 | 61 | empty |
| 2 | 743 | 0.68 | 0.76 | 58 | empty |
| 3 | 223 | 0.51 | 0.76 | 32 | empty |
| 4 | 205 | 0.49 | 0.76 | 26 | ETA |
| 5 | 64 | 0.42 | 0.81 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–C · 2058 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1332 Ų buried · 9 hydrogen bonds · protein-protein
- A–R · 1265 Ų buried · 11 hydrogen bonds · protein-protein
- R–D · 494 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 d-amino, 1 disulfide, 1 modified (covalent ligand, D-amino acid, disulfide, nonstandard).
Compared structures
- 6DDF · 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 0.88
- 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 6DDF · PDBe 6DDF · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P42866
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