MolNFT v1 · #175971 · protein
Cryo-EM structure of the prostaglandin E receptor EP4 coupled to G protein
7D7M · Prostaglandin E2 receptor EP4 SUBTYPE,PROSTAGLANDIN E2…: “Cryo-EM structure of the prostaglandin E receptor EP4 coupled to G protein”. Electron microscopy, 1 ligand (P2E), 16 pockets (best druggability 0.84). MolNFT v1 #175971 on…
- PDB
- 7D7M
- Type
- protein
- Length
- 1,031 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin E2 receptor EP4 SUBTYPE,PROSTAGLANDIN E2 receptor EP4 subtype; Guanine…
- UniProt
- P35408, P62873, P59768, P63092
- Ligands
- P2E
- Pockets
- 16 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin E2 receptor EP4 SUBTYPE,PROSTAGLANDIN E2 receptor EP4 subtype | protein | 285 | 77% helix, 1% strand | P35408 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 40% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 54 | 54% helix, 0% strand | P59768 |
| D | Guanine nucleotide-binding protein G(S) subunit alpha isoforms SHORT,GUANINE nucleotide-binding protein G(S) subunit alpha isoforms SHORT,GUANINE nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 228 | 45% helix, 13% strand | P63092 |
| E | Nanobody NB35 | protein | 128 | 5% helix, 38% strand | — |
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 A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.84 | 0.92 | 46 | P2E |
| 2 | 634 | 0.81 | 0.86 | 52 | empty |
| 3 | 1084 | 0.74 | 0.77 | 69 | empty |
| 4 | 526 | 0.68 | 0.79 | 70 | empty |
| 5 | 117 | 0.66 | 0.89 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1444 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 1419 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1378 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 727 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 396 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7D7M · Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein · the same entry in another collection · chain E against E, 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
- P35408 · AlphaFold monomer V2.0 prediction for prostaglandin E2 receptor EP4 subtype (P35408) · a predicted model of the same protein · chain A against A, TM-score 0.89
- 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 0.83
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 P35408
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P63092
- Elsewhere: RCSB PDB 7D7M · PDBe 7D7M · UniProt P35408 · UniProt P62873 · UniProt P59768 · UniProt P63092
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