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Complex structure of prostaglandin D2 synthase at 1.95A.
Analyse Complex structure of prostaglandin D2 synthase at 1.95A. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VCQ
- Type
- protein
- Length
- 783 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione-requiring prostaglandin D synthase
- EC
- 5.3.99.2
- UniProt
- O60760
- Ligands
- GSH, D25
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) | protein | 198 | 59% helix, 10% strand | O60760 |
| D | Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) | protein | 189 | 54% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
- D25 · 3-phenyl-5-(1H-pyrazol-3-yl)isoxazole · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.80 | 0.83 | 88 | GSH, D25 |
| 2 | 1011 | 0.77 | 0.79 | 89 | GSH, D25 |
| 3 | 372 | 0.71 | 0.83 | 50 | empty |
| 4 | 122 | 0.62 | 0.87 | 22 | empty |
| 5 | 81 | 0.50 | 0.83 | 14 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1556 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1451 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 420 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 149 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2VCQ · Complex structure of prostaglandin D2 synthase at 1.95A. · 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 2VCQ · PDBe 2VCQ · UniProt O60760
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