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Cryo-EM structure of the evatanepag-bound EP2-gs complex

Analyse Cryo-EM structure of the evatanepag-bound EP2-gs complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CX4
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: GM9
Pockets: 11 · best druggability 0.85

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	74% helix, 2% strand	P43116
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	228	43% helix, 18% strand	P63092
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	340	8% helix, 47% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	58	59% helix, 0% strand	P59768
N	Nanobody-35	protein	128	7% helix, 45% strand	—

Ligands and binding sites

GM9 · 2-[3-[[(4-~{tert}-butylphenyl)methyl-pyridin-3-ylsulfonyl-amino]methyl]phenoxy]ethanoic acid · ligand · chains R

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	913	0.85	0.86	78	empty
2	324	0.83	0.93	36	GM9
3	831	0.75	0.80	66	empty
4	684	0.69	0.77	49	empty
5	337	0.63	0.79	48	empty

Interfaces

5 interfaces between chains.

B–G · 2258 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1448 Å² buried · 23 hydrogen bonds · protein-protein
R–A · 1154 Å² buried · 14 hydrogen bonds · protein-protein
A–N · 832 Å² buried · 8 hydrogen bonds · protein-protein
B–N · 561 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7CX4 · Cryo-EM structure of the Evatanepag-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 0.92
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 0.90

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 7CX4 · PDBe 7CX4 · UniProt P43116 · UniProt P63092 · UniProt P62873 · UniProt P59768

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