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First inhibitor complex structure of human hematopoietic prostaglandin D synthase
Analyse First inhibitor complex structure of human hematopoietic prostaglandin D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V40
- Type
- protein
- Length
- 792 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, O16, MG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutathione-requiring prostaglandin D synthase (EC 5.3.99.2) | protein | 198 | 54% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, D, B, C
- O16 · 3-(1,3-benzothiazol-2-yl)-2-(1,4-dioxo-1,2,3,4-tetrahydrophthalazin-6-yl)-5-[(E)-2-phenylvinyl]-3H-tetraazol-2-ium · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D, B, C
- GOL · Glycerol · additive · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.77 | 0.79 | 82 | MG, GSH, O16, GOL |
| 2 | 1009 | 0.77 | 0.79 | 77 | MG, GSH, O16 |
| 3 | 951 | 0.72 | 0.76 | 59 | GOL |
| 4 | 136 | 0.59 | 0.84 | 27 | empty |
| 5 | 84 | 0.50 | 0.83 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1408 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1406 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 304 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1V40 · First Inhibitor Complex Structure of Human 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 1V40 · PDBe 1V40 · UniProt O60760
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