Research workbench
Cryo-EM Structure of the Prostaglandin E2 Receptor 4 Coupled to G Protein
Analyse Cryo-EM Structure of the Prostaglandin E2 Receptor 4 Coupled to G Protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8GDB
- Type
- protein
- Length
- 1,037 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Homo sapiens; Lama glama
- Molecule
- Guanine nucleotide-binding protein G(s) subunit alpha isoforms short; Guanine…
- UniProt
- P63092, P62873, A0A7J7XNR4, P35408
- Ligands
- P2E
- Pockets
- 12 · best druggability 0.86
Structure
electron microscopy · resolution 3.1 · 5 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | protein | 231 | 43% helix, 18% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 48% strand | P62873 |
| G | Guanine nucleotide-binding protein subunit gamma | protein | 58 | 53% helix, 0% strand | A0A7J7XNR4 |
| N | NB35 | protein | 126 | 5% helix, 38% strand | — |
| R | Prostaglandin E2 receptor EP4 subtype | protein | 283 | 78% helix, 1% strand | P35408 |
Ligands and binding sites
- P2E · (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.86 | 0.93 | 48 | P2E |
| 2 | 1051 | 0.85 | 0.86 | 81 | empty |
| 3 | 976 | 0.72 | 0.76 | 66 | empty |
| 4 | 584 | 0.68 | 0.78 | 70 | empty |
| 5 | 663 | 0.68 | 0.76 | 48 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2004 Ų buried · 6 hydrogen bonds · protein-protein
- A–R · 1432 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1388 Ų buried · 16 hydrogen bonds · protein-protein
- A–N · 664 Ų buried · 7 hydrogen bonds · protein-protein
- B–N · 414 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 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
- P35408 · AlphaFold monomer V2.0 prediction for prostaglandin E2 receptor EP4 subtype (P35408) · a predicted model of the same protein · chain R against A, TM-score 0.91
- P63092 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P63092
- Every structure of UniProt P62873
- Every structure of UniProt A0A7J7XNR4
- Every structure of UniProt P35408
- Elsewhere: RCSB PDB 8GDB · PDBe 8GDB · UniProt P63092 · UniProt P62873 · UniProt A0A7J7XNR4 · UniProt P35408
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