MolNFT v1 · #51621 · protein
Complex structure of prostaglandin D2 synthase at 1.95A.
2VCW · Glutathione-requiring prostaglandin D synthase: “Complex structure of prostaglandin D2 synthase at 1.95A.”. X-ray diffraction, 2 ligands (GSH, ZZA), 8 pockets (best druggability 0.77). MolNFT v1 #51621 on GenesisL1: 3D structure…
- PDB
- 2VCW
- Type
- protein
- Length
- 766 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, ZZA
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) | protein | 198 | 56% helix, 10% strand | O60760 |
| C | Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) | protein | 189 | 52% helix, 11% strand | O60760 |
| D | Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) | protein | 181 | 55% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 3 copies · chains A, B, C, D
- ZZA · 1-phenyl-1H-pyrazole-4-carboxylic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 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 | 0.77 | 0.80 | 88 | GSH, ZZA |
| 2 | 851 | 0.74 | 0.78 | 83 | GSH |
| 3 | 187 | 0.72 | 0.89 | 33 | empty |
| 4 | 146 | 0.66 | 0.87 | 25 | empty |
| 5 | 271 | 0.66 | 0.83 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1413 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1340 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 403 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 140 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2VCW · Complex structure of prostaglandin D2 synthase at 1.95A. · the same entry in another collection · chain D against D, TM-score 1.00
- O60760 · AlphaFold monomer V2.0 prediction for hematopoietic prostaglandin D synthase (O60760) · a predicted model of the same protein · chain C 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 2VCW · PDBe 2VCW · UniProt O60760
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