MolNFT v1 · #175638 · protein
Cryo-EM structure of the PGE2-bound EP2-gs complex
7CX2 · Prostaglandin E2 receptor EP2 subtype: “Cryo-EM structure of the PGE2-bound EP2-gs complex”. Electron microscopy, 1 ligand (P2E), 10 pockets (best druggability 0.84). MolNFT v1 #175638 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7CX2
- Type
- protein
- Length
- 1,020 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin E2 receptor EP2 subtype; Guanine nucleotide-binding protein G(S) subunit…
- UniProt
- P43116, P63092, P62873, P59768
- Ligands
- P2E
- Pockets
- 10 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Prostaglandin E2 receptor EP2 subtype | protein | 266 | 73% helix, 2% strand | P43116 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 228 | 46% helix, 18% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 8% helix, 46% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 60% helix, 0% strand | P59768 |
| N | Nanobody-35 | protein | 128 | 7% helix, 45% 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 R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.84 | 0.86 | 78 | empty |
| 2 | 244 | 0.82 | 0.95 | 27 | P2E |
| 3 | 928 | 0.75 | 0.79 | 62 | empty |
| 4 | 1044 | 0.73 | 0.76 | 72 | empty |
| 5 | 566 | 0.70 | 0.79 | 67 | empty |
Interfaces
5 interfaces between chains.
- B–G · 2208 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1420 Ų buried · 22 hydrogen bonds · protein-protein
- R–A · 1266 Ų buried · 23 hydrogen bonds · protein-protein
- A–N · 843 Ų buried · 7 hydrogen bonds · protein-protein
- B–N · 566 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7CX2 · Cryo-EM structure of the PGE2-bound EP2-Gs complex · the same entry in another collection · chain N against N, 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 G against A, TM-score 0.93
- P43116 · AlphaFold monomer V2.0 prediction for prostaglandin E2 receptor EP2 subtype (P43116) · a predicted model of the same protein · chain R against A, TM-score 0.91
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 P43116
- Every structure of UniProt P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7CX2 · PDBe 7CX2 · UniProt P43116 · UniProt P63092 · UniProt P62873 · UniProt P59768
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