MolNFT v1 · #189381 · protein
Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with C48/80, STATE2
7VDH · Mas-related G-protein coupled receptor member X2: “Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with C48/80, STATE2”. Electron microscopy, 2 ligands (CLR, 6IB), 13 pockets (best druggability 0.82). MolNFT v1 #189381…
- PDB
- 7VDH
- Type
- protein
- Length
- 1,109 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, 6IB
- Pockets
- 13 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Mas-related G-protein coupled receptor member X2 | protein | 267 | 81% helix, 0% strand | Q96LB1 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 45% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 7% helix, 46% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 60% helix, 0% strand | P59768 |
| S | Scfv | protein | 230 | 3% helix, 50% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains R
- 6IB · 2-[4-methoxy-3-[[2-methoxy-3-[[2-methoxy-5-[2-(methylamino)ethyl]phenyl]methyl]-5-[2-(methylamino) ethyl]phenyl]methyl]phenyl]-~{N}-methyl-ethanamine · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.82 | 0.85 | 66 | empty |
| 2 | 836 | 0.74 | 0.78 | 75 | empty |
| 3 | 192 | 0.56 | 0.80 | 30 | empty |
| 4 | 180 | 0.54 | 0.79 | 24 | empty |
| 5 | 81 | 0.52 | 0.85 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2212 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1215 Ų buried · 14 hydrogen bonds · protein-protein
- R–A · 1197 Ų buried · 10 hydrogen bonds · protein-protein
- A–S · 622 Ų buried · 9 hydrogen bonds · protein-protein
- B–S · 450 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7VDH · Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with C48/80, state2 · 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 1.00
- 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 0.94
- 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 Q96LB1
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7VDH · PDBe 7VDH · UniProt Q96LB1 · UniProt P63096 · UniProt P62873 · UniProt P59768
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.