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Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and an antagonist br-derivative

Analyse Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YHL
Type: protein
Length: 717 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prostaglandin E2 receptor EP4 subtype; Heavy chain of Fab fragment; Light chain of Fab…
UniProt: P35408
Ligands: 8VL
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prostaglandin E2 receptor EP4 subtype	protein	280	74% helix, 3% strand	P35408
H	Heavy chain of Fab fragment	protein	223	4% helix, 54% strand	—
L	Light chain of Fab fragment	protein	214	6% helix, 51% strand	—

Ligands and binding sites

8VL · 4-[2-[[(2R)-2-(4-bromanylnaphthalen-1-yl) propanoyl]amino]-4-cyano-phenyl]butanoic acid · ligand · chains A, H

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	404	0.81	0.89	48	8VL
2	472	0.58	0.74	51	empty
3	201	0.53	0.78	31	empty
4	195	0.49	0.76	24	empty
5	151	0.48	0.77	26	empty

Interfaces

3 interfaces between chains.

H–L · 1996 Å² buried · 15 hydrogen bonds · protein-protein
A–H · 683 Å² buried · 9 hydrogen bonds · protein-protein
A–L · 149 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5YHL · Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and an… · the same entry in another collection · chain A against A, TM-score 1.00
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 0.96

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
Elsewhere: RCSB PDB 5YHL · PDBe 5YHL · UniProt P35408

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