Research workbench
Cryoem structure of gq-coupled MRGPRX2 with small molecule agonist (R)-zinc-3573
Analyse Cryoem structure of gq-coupled MRGPRX2 with small molecule agonist (R)-zinc-3573 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S8N
- Type
- protein
- Length
- 1,090 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gs-mini-gq chimera; Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1…
- UniProt
- P62873, P59768, Q96LB1
- Ligands
- 8IU
- Pockets
- 14 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Gs-mini-gq chimera | protein | 221 | 44% helix, 18% strand | — |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 337 | 7% helix, 48% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 51 | 53% helix, 0% strand | P59768 |
| R | Mas-related G-protein coupled receptor member X2 | protein | 250 | 82% helix, 0% strand | Q96LB1 |
| E | SCFV16 | protein | 231 | 1% 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
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.83 | 0.84 | 71 | empty |
| 2 | 57 | 0.70 | 0.97 | 15 | empty |
| 3 | 525 | 0.63 | 0.75 | 52 | empty |
| 4 | 319 | 0.63 | 0.79 | 41 | empty |
| 5 | 236 | 0.58 | 0.79 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2007 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 1047 Ų buried · 5 hydrogen bonds · protein-protein
- B–R · 1015 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 532 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 391 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7S8N · CryoEM structure of Gq-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 0.95
- 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 D against A, TM-score 0.84
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 P62873
- Every structure of UniProt P59768
- Every structure of UniProt Q96LB1
- Elsewhere: RCSB PDB 7S8N · PDBe 7S8N · UniProt P62873 · UniProt P59768 · UniProt Q96LB1
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