Research workbench
Cryo-EM structure of a monomeric GPCR-gi complex with small molecule
Analyse Cryo-EM structure of a monomeric GPCR-gi complex with small molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W0M
- Type
- protein
- Length
- 1,134 residues
- Chains
- 5
- 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, P35414
- Ligands
- 8EH
- Pockets
- 17 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 44% helix, 14% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 46% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 53% helix, 0% strand | P59768 |
| R | Soluble cytochrome B562,APELIN receptor | protein | 290 | 70% helix, 3% strand | P35414 |
| S | SCFV16 | protein | 233 | 3% helix, 30% strand | — |
Ligands and binding sites
- 8EH · (1R,2S)-N-[4-(2,6-dimethoxyphenyl)-5-(6-methylpyridin-2-yl)-1,2,4-triazol-3-yl]-1-(5-methylpyrimidin-2-yl)-1-oxidanyl-propane-2-sulfonamide · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.82 | 0.83 | 68 | empty |
| 2 | 953 | 0.77 | 0.79 | 61 | 8EH |
| 3 | 167 | 0.74 | 0.91 | 30 | empty |
| 4 | 82 | 0.68 | 0.93 | 21 | empty |
| 5 | 733 | 0.67 | 0.75 | 76 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2047 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1100 Ų buried · 5 hydrogen bonds · protein-protein
- A–R · 853 Ų buried · 5 hydrogen bonds · protein-protein
- A–S · 523 Ų buried · 5 hydrogen bonds · protein-protein
- B–S · 449 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7W0M · Cryo-EM structure of a monomeric GPCR-Gi complex with small molecule · 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
- P35414 · AlphaFold monomer V2.0 prediction for apelin receptor (P35414) · a predicted model of the same protein · chain R against A, TM-score 0.88
- 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 0.82
- 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 0.81
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 P35414
- Elsewhere: RCSB PDB 7W0M · PDBe 7W0M · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P35414
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