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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
- 2VCZ
- Type
- protein
- Length
- 771 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, VC3
- Pockets
- 7 · best druggability 0.77
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 | 57% helix, 10% strand | O60760 |
| C | Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) | protein | 177 | 51% helix, 11% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
- VC3 · 3-(4-nitrophenyl)-1H-pyrazole · ligand · chains B
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 | 1169 | 0.77 | 0.79 | 103 | GSH, VC3 |
| 2 | 343 | 0.77 | 0.87 | 39 | empty |
| 3 | 129 | 0.70 | 0.91 | 24 | empty |
| 4 | 551 | 0.69 | 0.78 | 53 | GSH |
| 5 | 260 | 0.57 | 0.78 | 34 | GSH |
Interfaces
4 interfaces between chains.
- A–B · 1410 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1356 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 584 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 206 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2VCZ · 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 2VCZ · PDBe 2VCZ · UniProt O60760
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