MolNFT v1 · #156610 · protein
Crystal structure of EP3 receptor bound to misoprostol-fa
6M9T · Prostaglandin E2 receptor EP3 subtype, endolysin chimera: “Crystal structure of EP3 receptor bound to misoprostol-fa”. X-ray diffraction, 3 ligands (OLA, J9P, SO4), 4 pockets (best druggability 0.85). MolNFT v1 #156610 on GenesisL1…
- PDB
- 6M9T
- Type
- protein
- Length
- 444 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin E2 receptor EP3 subtype, endolysin chimera
- EC
- 3.2.1.17
- UniProt
- P43115, P00720
- Ligands
- OLA, J9P, SO4
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin E2 receptor EP3 subtype, endolysin chimera (EC 3.2.1.17) | protein | 444 | 73% helix, 5% strand | P43115, P00720 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 4 copies · chains A
- J9P · (11alpha,12alpha,13E,16S)-11,16-dihydroxy-16-methyl-9-oxoprost-13-en-1-oic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.85 | 0.97 | 33 | J9P |
| 2 | 778 | 0.77 | 0.81 | 60 | empty |
| 3 | 74 | 0.33 | 0.75 | 13 | empty |
| 4 | 77 | 0.32 | 0.74 | 14 | SO4 |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6M9T · Crystal structure of EP3 receptor bound to misoprostol-FA · the same entry in another collection · chain A against A, TM-score 1.00
- P43115 · AlphaFold monomer V2.0 prediction for prostaglandin E2 receptor EP3 subtype (P43115) · a predicted model of the same protein · chain A against A, TM-score 0.60
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 P43115
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 6M9T · PDBe 6M9T · UniProt P43115 · UniProt P00720
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