Research workbench
Cryoem structure of gq-coupled MRGPRX4 with small molecule agonist MS47134
Analyse Cryoem structure of gq-coupled MRGPRX4 with small molecule agonist MS47134 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S8P
- Type
- protein
- Length
- 1,089 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, Q96LA9
- Ligands
- 8IX
- Pockets
- 7 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Gs-mini-gq chimera | protein | 222 | 47% helix, 18% strand | — |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 47% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 51 | 61% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 231 | 3% helix, 45% strand | — |
| R | Soluble cytochrome B562,MAS-related G-protein coupled receptor member X4 chimera | protein | 247 | 77% helix, 0% strand | Q96LA9 |
Ligands and binding sites
- 8IX · N-[(1R,3R,5S,7R)-3,5-dimethyltricyclo[3.3.1.1~3, 7~]decane-1-carbonyl]-D-phenylalanine · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.82 | 0.83 | 67 | empty |
| 2 | 749 | 0.74 | 0.80 | 98 | empty |
| 3 | 771 | 0.68 | 0.75 | 75 | empty |
| 4 | 315 | 0.62 | 0.79 | 32 | 8IX |
| 5 | 64 | 0.47 | 0.84 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2007 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1026 Ų buried · 4 hydrogen bonds · protein-protein
- B–R · 1020 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 565 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 405 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7S8P · CryoEM structure of Gq-coupled MRGPRX4 with small molecule agonist MS47134 · the same entry in another collection · chain B against B, 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
- Q96LA9 · AlphaFold monomer V2.0 prediction for mas-related G-protein coupled receptor member X4… · a predicted model of the same protein · chain R against A, TM-score 0.88
- 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 Q96LA9
- Elsewhere: RCSB PDB 7S8P · PDBe 7S8P · UniProt P62873 · UniProt P59768 · UniProt Q96LA9
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