Research workbench
Crystal structure of rat hematopoietic prostaglandin D synthase
Analyse Crystal structure of rat hematopoietic prostaglandin D synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y9Z
- Type
- protein
- Length
- 396 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hematopoietic prostaglandin D synthase
- EC
- 5.3.99.2, 2.5.1.18
- UniProt
- O35543
- Ligands
- GSH, MG
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 198 | 59% helix, 10% strand | O35543 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.77 | 0.79 | 89 | GSH, MG, DIO |
| 2 | 81 | 0.48 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1442 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5Y9Z · Crystal structure of rat hematopoietic prostaglandin D synthase · the same entry in another collection · chain B against B, TM-score 1.00
- O35543 · AlphaFold monomer V2.0 prediction for hematopoietic prostaglandin D synthase (O35543) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O35543
- Elsewhere: RCSB PDB 5Y9Z · PDBe 5Y9Z · UniProt O35543
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