MolNFT v1 · #141107 · protein
Crystal structure of hematopoietic prostaglandin D synthase apo form
5YWE: “Crystal structure of hematopoietic prostaglandin D synthase apo form”. X-ray diffraction, 2 ligands (GSH, MG), 5 pockets (best druggability 0.79). MolNFT v1 #141107 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YWE
- Type
- protein
- Length
- 792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hematopoietic prostaglandin D synthase
- EC
- 5.3.99.2, 2.5.1.18
- UniProt
- O60760
- Ligands
- GSH, MG
- Pockets
- 5 · 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 | Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18) | protein | 198 | 57% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.79 | 0.82 | 78 | GSH, MG |
| 2 | 1189 | 0.76 | 0.78 | 85 | GSH, MG |
| 3 | 970 | 0.73 | 0.76 | 56 | GOL |
| 4 | 81 | 0.51 | 0.84 | 21 | empty |
| 5 | 85 | 0.51 | 0.84 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1428 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1427 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 328 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5YWE · Crystal structure of hematopoietic prostaglandin D synthase apo form · 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 5YWE · PDBe 5YWE · UniProt O60760
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.