Research workbench
Cryoem structure of gi-coupled MRGPRX2 with peptide agonist cortistatin-14
Analyse Cryoem structure of gi-coupled MRGPRX2 with peptide agonist cortistatin-14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S8M
- Type
- protein
- Length
- 1,102 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
- Pockets
- 11 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 45% helix, 18% strand | P63096 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 7% helix, 46% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 58% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 232 | 3% helix, 46% strand | — |
| R | Soluble cytochrome B562, mas-related G-protein coupled receptor member X2 chimera | protein | 253 | 82% helix, 0% strand | Q96LB1 |
| A | Cortistatin 14 | protein | 5 | 0% helix, 0% strand | — |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.82 | 0.85 | 66 | empty |
| 2 | 946 | 0.72 | 0.76 | 89 | empty |
| 3 | 245 | 0.58 | 0.79 | 29 | empty |
| 4 | 178 | 0.56 | 0.81 | 30 | empty |
| 5 | 122 | 0.54 | 0.81 | 14 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2159 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1175 Ų buried · 14 hydrogen bonds · protein-protein
- B–R · 1146 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 568 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 478 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7S8M · CryoEM structure of Gi-coupled MRGPRX2 with peptide agonist Cortistatin-14 · the same entry in another collection · chain A 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 C against A, TM-score 1.00
- 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 0.95
- 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
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain B 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
- Elsewhere: RCSB PDB 7S8M · PDBe 7S8M · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt Q96LB1
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