Research workbench
Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with pamp-12. STATE1
Analyse Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with pamp-12.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VUY
- Type
- protein
- Length
- 1,112 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mas-related G-protein coupled receptor member X2; Guanine nucleotide-binding protein G(I)…
- UniProt
- Q96LB1, P63096, P62873, P59768
- Ligands
- CLR
- Pockets
- 10 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Mas-related G-protein coupled receptor member X2 | protein | 258 | 84% helix, 0% strand | Q96LB1 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 226 | 43% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 43% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 52% helix, 0% strand | P59768 |
| S | Scfv | protein | 233 | 5% helix, 44% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.81 | 0.85 | 62 | empty |
| 2 | 1136 | 0.76 | 0.79 | 93 | empty |
| 3 | 301 | 0.64 | 0.81 | 51 | empty |
| 4 | 255 | 0.58 | 0.78 | 21 | empty |
| 5 | 167 | 0.49 | 0.77 | 19 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2175 Ų buried · 14 hydrogen bonds · protein-protein
- R–A · 1278 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1183 Ų buried · 11 hydrogen bonds · protein-protein
- A–S · 615 Ų buried · 7 hydrogen bonds · protein-protein
- B–S · 478 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7VUY · Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with PAMP-12. state1 · the same entry in another collection · chain S against S, 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
- 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 G against A, TM-score 0.92
- 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 0.83
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 7VUY · PDBe 7VUY · UniProt Q96LB1 · UniProt P63096 · UniProt P62873 · UniProt P59768
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