MolNFT v1 · #189210 · protein
Cry-EM structure of M4-C110-G protein complex
7V6A · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Cry-EM structure of M4-C110-G protein complex”. Electron microscopy, 1 ligand (5XI), 18 pockets (best druggability 0.83). MolNFT v1 #189210 on GenesisL1: 3D structure…
- PDB
- 7V6A
- Type
- protein
- Length
- 1,122 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, P08173
- Ligands
- 5XI
- Pockets
- 18 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 44% helix, 12% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 38% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 42% helix, 0% strand | P59768 |
| S | SCFV16 | protein | 232 | 0% helix, 35% strand | — |
| R | Muscarinic acetylcholine receptor M4 | protein | 277 | 76% helix, 0% strand | P08173 |
Ligands and binding sites
- 5XI · methyl 4-[4-(3-methyl-2-oxidanylidene-benzimidazol-1-yl)piperidin-1-yl]piperidine-1-carboxylate · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.83 | 0.85 | 58 | empty |
| 2 | 267 | 0.78 | 0.90 | 39 | 5XI |
| 3 | 717 | 0.71 | 0.78 | 68 | empty |
| 4 | 124 | 0.57 | 0.84 | 23 | empty |
| 5 | 188 | 0.56 | 0.80 | 31 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2154 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1125 Ų buried · 12 hydrogen bonds · protein-protein
- A–R · 896 Ų buried · 4 hydrogen bonds · protein-protein
- A–S · 594 Ų buried · 11 hydrogen bonds · protein-protein
- B–S · 465 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7V6A · Cry-EM structure of M4-c110-G 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 0.99
- P08173 · AlphaFold monomer V2.0 prediction for muscarinic acetylcholine receptor M4 (P08173) · a predicted model of the same protein · chain R against A, TM-score 0.91
- 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 P08173
- Elsewhere: RCSB PDB 7V6A · PDBe 7V6A · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P08173
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