Research workbench
Cryo-EM structure of a monomeric GPCR-gi complex with peptide
Analyse Cryo-EM structure of a monomeric GPCR-gi complex with peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W0O
- Type
- protein
- Length
- 1,159 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, P0DMC3, P35414
- Pockets
- 17 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 225 | 43% helix, 12% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 42% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 56% helix, 0% strand | P59768 |
| D | Apelin receptor early endogenous ligand | protein | 15 | 0% helix, 0% strand | P0DMC3 |
| R | Soluble cytochrome B562,APELIN receptor | protein | 293 | 68% helix, 1% strand | P35414 |
| S | SCFV16 | protein | 233 | 3% helix, 35% strand | — |
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.83 | 0.85 | 102 | empty |
| 2 | 1102 | 0.82 | 0.83 | 69 | empty |
| 3 | 873 | 0.77 | 0.80 | 95 | empty |
| 4 | 94 | 0.71 | 0.94 | 27 | empty |
| 5 | 118 | 0.68 | 0.90 | 30 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1938 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1146 Ų buried · 4 hydrogen bonds · protein-protein
- D–R · 825 Ų buried · 5 hydrogen bonds · protein-protein
- A–R · 822 Ų buried · 1 hydrogen bond · protein-protein
- A–S · 527 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7W0O · Cryo-EM structure of a monomeric GPCR-Gi complex with peptide · 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 0.97
- P35414 · AlphaFold monomer V2.0 prediction for apelin receptor (P35414) · a predicted model of the same protein · chain R against A, TM-score 0.85
- 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 0.80
- 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 C against A, TM-score 0.80
- P0DMC3 · AlphaFold monomer V2.0 prediction for apelin receptor early endogenous ligand (P0DMC3) · a predicted model of the same protein · chain D against A, TM-score 0.21
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 P0DMC3
- Every structure of UniProt P35414
- Elsewhere: RCSB PDB 7W0O · PDBe 7W0O · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P0DMC3 · UniProt P35414
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