MolNFT v1 · #10670 · protein
Crystal structure of hematopoietic prostaglandin D synthase
1IYH: “Crystal structure of hematopoietic prostaglandin D synthase”. X-ray diffraction, 2 ligands (GSH, MG), 6 pockets (best druggability 0.79). MolNFT v1 #10670 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1IYH
- 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
- UniProt
- O60760
- Ligands
- GSH, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hematopoietic prostaglandin D synthase (EC 5.3.99.2) | protein | 198 | 56% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.79 | 0.81 | 93 | MG, GSH |
| 2 | 1171 | 0.76 | 0.78 | 87 | MG, GSH |
| 3 | 416 | 0.70 | 0.81 | 44 | GSH |
| 4 | 125 | 0.62 | 0.86 | 25 | empty |
| 5 | 128 | 0.62 | 0.86 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1418 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1395 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 473 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1IYH · Crystal structure of hematopoietic prostaglandin D synthase · 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 1IYH · PDBe 1IYH · UniProt O60760
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