MolNFT v1 · #141126 · protein
Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and ono-AE3-208
5YWY · Prostaglandin E2 receptor EP4 SUBTYPE,PROSTAGLANDIN E2…: “Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and ono-AE3-208”. X-ray diffraction, 1 ligand (7UR), 8 pockets (best druggability 0.80).…
- PDB
- 5YWY
- 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,PROSTAGLANDIN E2 receptor EP4 subtype; Heavy chain…
- UniProt
- P35408
- Ligands
- 7UR
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin E2 receptor EP4 SUBTYPE,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, 52% strand | — |
Ligands and binding sites
- 7UR · 4-[4-cyano-2-[[(2R)-2-(4-fluoranylnaphthalen-1-yl) propanoyl]amino]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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.80 | 0.89 | 44 | 7UR |
| 2 | 521 | 0.60 | 0.74 | 47 | empty |
| 3 | 207 | 0.54 | 0.78 | 31 | empty |
| 4 | 208 | 0.50 | 0.76 | 23 | empty |
| 5 | 146 | 0.48 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2018 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 694 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 156 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5YWY · Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and… · 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 5YWY · PDBe 5YWY · UniProt P35408
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