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Crystal structure of prostaglandin D2 synthase in complex with fragment 1A at 1.84A resolution.
Analyse Crystal structure of prostaglandin D2 synthase in complex with fragment 1A at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZTC
- Type
- protein
- Length
- 399 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
- O60760
- Ligands
- GSH, QPN, MG
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 56% 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 | 199 | 56% helix, 10% strand | O60760 |
| B | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 200 | 56% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains A, B
- QPN · 1-[1-(3-fluorophenyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-5-yl]propan-1-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- GOL · Glycerol · additive · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.79 | 0.81 | 96 | GSH, MG, QPN, GOL |
| 2 | 114 | 0.65 | 0.89 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1446 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6ZTC · Crystal structure of prostaglandin D2 synthase in complex with fragment 1A at 1.84A… · the same entry in another collection · chain A against A, TM-score 1.00
- O60760 · AlphaFold monomer V2.0 prediction for hematopoietic prostaglandin D synthase (O60760) · 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 O60760
- Elsewhere: RCSB PDB 6ZTC · PDBe 6ZTC · UniProt O60760
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