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Complex structure of prostaglandin D2 synthase at 2.25A.
Analyse Complex structure of prostaglandin D2 synthase at 2.25A. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VD1
- Type
- protein
- Length
- 777 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, D28, MG
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) | protein | 198 | 55% helix, 10% strand | O60760 |
| C | Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) | protein | 183 | 53% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
- D28 · 4-{[4-(4-fluoro-3-methylphenyl)-1,3-thiazol-2-yl]amino}-2-hydroxybenzoic acid · ligand · chains B
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.79 | 0.81 | 95 | GSH, D28, MG |
| 2 | 346 | 0.77 | 0.87 | 39 | empty |
| 3 | 667 | 0.73 | 0.80 | 64 | GSH |
| 4 | 109 | 0.67 | 0.90 | 24 | empty |
| 5 | 422 | 0.63 | 0.77 | 43 | GSH |
Interfaces
4 interfaces between chains.
- A–B · 1424 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1400 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 591 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 188 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2VD1 · Complex structure of prostaglandin D2 synthase at 2.25A. · 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 2VD1 · PDBe 2VD1 · UniProt O60760
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