Research workbench
rat hPGDS complexed with a quinoline
Analyse rat hPGDS complexed with a quinoline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N69
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Rattus norvegicus
- Molecule
- Hematopoietic prostaglandin D synthase
- EC
- 5.3.99.2, 2.5.1.18
- UniProt
- O35543
- Ligands
- GSH, KDV
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 198 | 59% helix, 11% strand | O35543 |
| B | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 199 | 59% helix, 9% strand | O35543 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, B
- KDV · quinoline-3-carbonitrile · ligand · 2 copies · chains A, B
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 | 1123 | 0.78 | 0.79 | 88 | GSH, KDV |
| 2 | 93 | 0.43 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1382 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 6N69 · PDBe 6N69 · UniProt O35543
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