Research workbench
Complex structure of prostaglandin D2 synthase at 2.2A.
Analyse Complex structure of prostaglandin D2 synthase at 2.2A. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VD0
- Type
- protein
- Length
- 792 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, D27
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) | protein | 198 | 57% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 3 copies · chains A, B, C, D
- D27 · 2-{[(2E)-3-(3,4-dimethoxyphenyl)prop-2-enoyl]amino}benzoic acid · ligand · chains B
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.79 | 0.81 | 89 | GSH |
| 2 | 1131 | 0.77 | 0.79 | 95 | GSH, D27 |
| 3 | 344 | 0.75 | 0.86 | 43 | GOL |
| 4 | 122 | 0.66 | 0.89 | 27 | empty |
| 5 | 121 | 0.65 | 0.88 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1412 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1404 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 589 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 179 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2VD0 · Complex structure of prostaglandin D2 synthase at 2.2A. · 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 2VD0 · PDBe 2VD0 · UniProt O60760
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