Research workbench
Complex of human hematopoietic prostagandin D2 synthase (hh- pgds) in complex with an active site inhibitor.
Analyse Complex of human hematopoietic prostagandin D2 synthase (hh- pgds) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AIV
- 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
- M1W, GSH, MG
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 55% 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 | 55% helix, 10% strand | O60760 |
Ligands and binding sites
- M1W · 3-(1H-indol-4-yl)-N-(3-methoxypropyl)-1,2,4-oxadiazole-5-carboxamide · ligand · 4 copies · chains A, B, C, D
- GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.80 | 0.82 | 98 | M1W, GSH, MG |
| 2 | 954 | 0.78 | 0.80 | 88 | M1W, GSH, MG |
| 3 | 452 | 0.74 | 0.83 | 59 | empty |
| 4 | 105 | 0.61 | 0.87 | 27 | empty |
| 5 | 58 | 0.31 | 0.75 | 11 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1425 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1401 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 125 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5AIV · Complex of human hematopoietic prostagandin D2 synthase (hH-PGDS) in complex with an… · 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 5AIV · PDBe 5AIV · UniProt O60760
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