Research workbench
Xfel crystal structure of the prostaglandin D2 receptor CRTH2 in complex with 15R-methyl-PGD2
Analyse Xfel crystal structure of the prostaglandin D2 receptor CRTH2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M8W
- Type
- protein
- Length
- 437 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin D2 receptor 2, endolysin chimera
- UniProt
- Q9Y5Y4, D9IEF7
- Ligands
- YSS, NA, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin D2 receptor 2, endolysin chimera | protein | 437 | 73% helix, 2% strand | Q9Y5Y4, D9IEF7 |
Ligands and binding sites
- YSS · 15R-methyl-prostaglandin D2 · ligand · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- FLC · Citrate anion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.78 | 0.86 | 41 | YSS |
| 2 | 574 | 0.68 | 0.78 | 40 | FLC, SO4 |
| 3 | 117 | 0.50 | 0.80 | 20 | empty |
| 4 | 132 | 0.44 | 0.76 | 23 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, alkylation).
Compared structures
- 7M8W · XFEL crystal structure of the prostaglandin D2 receptor CRTH2 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5Y4 · AlphaFold monomer V2.0 prediction for prostaglandin D2 receptor 2 (Q9Y5Y4) · a predicted model of the same protein · chain A against A, TM-score 0.72
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 Q9Y5Y4
- Every structure of UniProt D9IEF7
- Elsewhere: RCSB PDB 7M8W · PDBe 7M8W · UniProt Q9Y5Y4 · UniProt D9IEF7
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