MolNFT v1 · #187380 · protein
PZM21 bound mu opioid receptor-gi protein complex
7SBF · Guanine nucleotide-binding protein G(I) subunit alpha-1: “PZM21 bound mu opioid receptor-gi protein complex”. Electron microscopy, 1 ligand (8QY), 11 pockets (best druggability 0.82). MolNFT v1 #187380 on GenesisL1: 3D structure…
- PDB
- 7SBF
- Type
- protein
- Length
- 1,119 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
- 8QY
- Pockets
- 11 · best druggability 0.82
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 | 217 | 43% helix, 18% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 8% helix, 46% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 53% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 232 | 4% helix, 48% strand | — |
| R | Soluble cytochrome B562, mu-type opioid receptor chimera, mu-type opioid receptor | protein | 281 | 78% helix, 1% strand | P42866 |
Ligands and binding sites
- 8QY · N-[(2S)-2-(dimethylamino)-3-(4-hydroxyphenyl)propyl]-N'-[(2S)-1-(thiophen-3-yl)propan-2-yl]urea · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.82 | 0.85 | 61 | empty |
| 2 | 634 | 0.75 | 0.81 | 41 | 8QY |
| 3 | 854 | 0.69 | 0.75 | 67 | empty |
| 4 | 193 | 0.55 | 0.79 | 30 | empty |
| 5 | 172 | 0.53 | 0.79 | 28 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1984 Ų buried · 8 hydrogen bonds · protein-protein
- A–R · 1296 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1144 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 547 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 429 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7SBF · PZM21 bound Mu Opioid Receptor-Gi Protein 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 1.00
- 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 0.96
- 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 0.95
- 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 7SBF · PDBe 7SBF · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P42866
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