MolNFT v1 · #18067 · protein
Crystal structure of hematopoietic prostaglandin D synthase complex with glutathione
1PD2: “Crystal structure of hematopoietic prostaglandin D synthase complex with glutathione”. X-ray diffraction, 1 ligand (GSH), 2 pockets (best druggability 0.77). MolNFT v1 #18067 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1PD2
- Type
- protein
- Length
- 398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hematopoietic prostaglandin D synthase
- EC
- 5.3.99.2
- UniProt
- O35543
- Ligands
- GSH
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2 | Hematopoietic prostaglandin D synthase (EC 5.3.99.2) | protein | 199 | 55% helix, 10% strand | O35543 |
Ligands and binding sites
- GSH · Glutathione · ligand · 2 copies · chains 1, 2
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.77 | 0.79 | 91 | GSH |
| 2 | 89 | 0.53 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- 1–2 · 1304 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1PD2 · Crystal structure of hematopoietic prostaglandin D synthase complex with glutathione · the same entry in another collection · chain 1 against 1, TM-score 1.00
- O35543 · AlphaFold monomer V2.0 prediction for hematopoietic prostaglandin D synthase (O35543) · a predicted model of the same protein · chain 1 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 O35543
- Elsewhere: RCSB PDB 1PD2 · PDBe 1PD2 · UniProt O35543
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