Research workbench

Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with substance P

Analyse Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with substance P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VDM
Type: protein
Length: 1,096 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
UniProt: P63096, P62873, P59768, Q96LB1, P20366
Ligands: CLR
Pockets: 13 · best druggability 0.82

Structure

electron microscopy · 6 distinct chains · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(I) subunit alpha-1	protein	217	42% helix, 17% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	8% helix, 45% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	55	53% helix, 0% strand	P59768
S	Scfv	protein	229	3% helix, 46% strand	—
R	Mas-related G-protein coupled receptor member X2	protein	253	78% helix, 0% strand	Q96LB1
L	Peptide from protachykinin-1	protein	3	0% helix, 0% strand	P20366

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

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	761	0.82	0.86	63	empty
2	961	0.76	0.79	86	empty
3	360	0.68	0.81	29	empty
4	174	0.56	0.80	27	empty
5	195	0.54	0.79	27	empty

Interfaces

7 interfaces between chains.

B–G · 2189 Å² buried · 15 hydrogen bonds · protein-protein
A–R · 1209 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1188 Å² buried · 15 hydrogen bonds · protein-protein
A–S · 598 Å² buried · 12 hydrogen bonds · protein-protein
B–S · 436 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7VDM · Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with substance P · the same entry in another collection · chain L against L, TM-score 1.00
P20366 · AlphaFold monomer V2.0 prediction for protachykinin-1 (P20366) · a predicted model of the same protein · chain L against A, 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 0.94
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 P63096
Every structure of UniProt P62873
Every structure of UniProt P59768
Every structure of UniProt Q96LB1
Every structure of UniProt P20366
Elsewhere: RCSB PDB 7VDM · PDBe 7VDM · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt Q96LB1 · UniProt P20366

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