MolNFT v1 · #187302 · protein
Cryoem structure of gi-coupled MRGPRX2 with small molecule agonist (R)-zinc-3573
7S8O · Soluble cytochrome B562,MAS-related G-protein coupled…: “Cryoem structure of gi-coupled MRGPRX2 with small molecule agonist (R)-zinc-3573”. Electron microscopy, 1 ligand (8IU), 11 pockets (best druggability 0.82). MolNFT v1 #187302…
- PDB
- 7S8O
- Type
- protein
- Length
- 1,101 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562,MAS-related G-protein coupled receptor member X2 chimera; Guanine…
- UniProt
- Q96LB1, P63096, P62873, P59768
- Ligands
- 8IU
- Pockets
- 11 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Soluble cytochrome B562,MAS-related G-protein coupled receptor member X2 chimera | protein | 257 | 81% helix, 0% strand | Q96LB1 |
| B | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 42% helix, 18% strand | P63096 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 7% helix, 47% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 55% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 232 | 3% helix, 46% strand | — |
Ligands and binding sites
- 8IU · (3R)-N,N-dimethyl-1-[(8S)-5-phenylpyrazolo[1,5-a]pyrimidin-7-yl]pyrrolidin-3-amine · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.82 | 0.83 | 63 | empty |
| 2 | 54 | 0.70 | 0.98 | 15 | empty |
| 3 | 740 | 0.69 | 0.76 | 74 | empty |
| 4 | 295 | 0.58 | 0.78 | 37 | empty |
| 5 | 295 | 0.58 | 0.77 | 24 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2148 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1150 Ų buried · 10 hydrogen bonds · protein-protein
- R–B · 1107 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 529 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 403 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7S8O · CryoEM structure of Gi-coupled MRGPRX2 with small molecule agonist (R)-Zinc-3573 · the same entry in another collection · chain E against E, 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 C against A, TM-score 0.99
- Q96LB1 · AlphaFold monomer V2.0 prediction for mas-related G-protein coupled receptor member X2… · a predicted model of the same protein · chain R against A, TM-score 0.94
- 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 D against A, TM-score 0.84
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain B 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 Q96LB1
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7S8O · PDBe 7S8O · UniProt Q96LB1 · UniProt P63096 · UniProt P62873 · UniProt P59768
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