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The crystal structure of prostaglandin F synthase from trypanosoma brucei
Analyse The crystal structure of prostaglandin F synthase from trypanosoma brucei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VBJ
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin F synthase
- EC
- 1.1.1.188
- UniProt
- Q9GV41
- Ligands
- NAP
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prostaglandin F synthase (EC 1.1.1.188) | protein | 281 | 41% helix, 15% strand | Q9GV41 |
| B | Prostaglandin F synthase (EC 1.1.1.188) | protein | 279 | 40% helix, 16% strand | Q9GV41 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.76 | 0.90 | 26 | empty |
| 2 | 239 | 0.66 | 0.83 | 35 | NAP, CIT |
| 3 | 241 | 0.63 | 0.81 | 38 | NAP, CIT |
| 4 | 137 | 0.48 | 0.78 | 26 | empty |
| 5 | 127 | 0.46 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1VBJ · The crystal structure of prostaglandin F synthase from Trypanosoma brucei · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GV41 · AlphaFold monomer V2.0 prediction for 9,11-endoperoxide prostaglandin H2 reductase… · a predicted model of the same protein · chain B 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 Q9GV41
- Elsewhere: RCSB PDB 1VBJ · PDBe 1VBJ · UniProt Q9GV41
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