Research workbench
Crystal structure analysis of human hematopoietic prostaglandin D synthase complexed with hql-79
Analyse Crystal structure analysis of human hematopoietic prostaglandin D synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CVD
- 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
- UniProt
- O60760
- Ligands
- GSH, HQL, MG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutathione-requiring prostaglandin D synthase | protein | 198 | 56% helix, 10% strand | O60760 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, D, B, C
- HQL · 4-(benzhydryloxy)-1-[3-(1H-tetraazol-5-yl) propyl]piperidine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D, B, C
- GOL · Glycerol · additive · 7 copies · chains A, B, C, 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 | 1058 | 0.81 | 0.81 | 95 | MG, GSH, HQL |
| 2 | 1142 | 0.80 | 0.81 | 108 | GSH, HQL |
| 3 | 893 | 0.72 | 0.77 | 56 | GOL |
| 4 | 119 | 0.62 | 0.87 | 23 | empty |
| 5 | 86 | 0.51 | 0.84 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1458 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1453 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 286 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2CVD · Crystal structure analysis of human hematopoietic prostaglandin D synthase complexed with… · 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 0.98
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 2CVD · PDBe 2CVD · UniProt O60760
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