Research workbench
Cryo-EM structure of a GPCR-gi complex with peptide
Analyse Cryo-EM structure of a 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
- 7W0P
- Type
- protein
- Length
- 1,158 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, P35414, P0DMC3
- Pockets
- 18 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 225 | 44% helix, 15% 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 | 56% helix, 0% strand | P59768 |
| R | Soluble cytochrome B562,APELIN receptor | protein | 292 | 74% helix, 0% strand | P35414 |
| S | SCFV16 | protein | 233 | 4% helix, 39% strand | — |
| D | Apelin receptor early endogenous ligand | protein | 15 | 27% helix, 0% strand | P0DMC3 |
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.82 | 0.85 | 64 | empty |
| 2 | 190 | 0.82 | 0.96 | 33 | empty |
| 3 | 55 | 0.71 | 0.98 | 21 | empty |
| 4 | 1128 | 0.71 | 0.75 | 80 | empty |
| 5 | 67 | 0.70 | 0.96 | 23 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2054 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1250 Ų buried · 8 hydrogen bonds · protein-protein
- R–D · 1054 Ų buried · 2 hydrogen bonds · protein-protein
- A–R · 1017 Ų buried · 7 hydrogen bonds · protein-protein
- A–S · 594 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7W0P · Cryo-EM structure of a GPCR-Gi complex with peptide · the same entry in another collection · chain D against D, 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
- 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 0.91
- P35414 · AlphaFold monomer V2.0 prediction for apelin receptor (P35414) · a predicted model of the same protein · chain R against A, TM-score 0.87
- 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
- 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 0.25
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
- Every structure of UniProt P0DMC3
- Elsewhere: RCSB PDB 7W0P · PDBe 7W0P · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P35414 · UniProt P0DMC3
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