Research workbench
Crystal structure of leukotriene B4 12- HYDROXYDEHYDROGENASE/15-oxo-prostaglandin 13-reductase in apo form
Analyse Crystal structure of leukotriene B4 12- HYDROXYDEHYDROGENASE/15-oxo-prostaglandi… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V3U
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leukotriene B4 12- HYDROXYDEHYDROGENASE/PROSTAGLANDIN 15-keto reductase
- EC
- 1.3.1.48
- UniProt
- Q9EQZ5
- Ligands
- CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leukotriene B4 12- HYDROXYDEHYDROGENASE/PROSTAGLANDIN 15-keto reductase (EC 1.3.1.48) | protein | 316 | 31% helix, 29% strand | Q9EQZ5 |
| B | Leukotriene B4 12- HYDROXYDEHYDROGENASE/PROSTAGLANDIN 15-keto reductase (EC 1.3.1.48) | protein | 332 | 31% helix, 27% strand | Q9EQZ5 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.79 | 0.96 | 37 | empty |
| 2 | 493 | 0.77 | 0.84 | 56 | CL |
| 3 | 572 | 0.76 | 0.83 | 72 | CL |
| 4 | 127 | 0.47 | 0.78 | 25 | empty |
| 5 | 52 | 0.34 | 0.78 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1198 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1V3U · Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9EQZ5 · AlphaFold monomer V2.0 prediction for prostaglandin reductase 1 (Q9EQZ5) · 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 Q9EQZ5
- Elsewhere: RCSB PDB 1V3U · PDBe 1V3U · UniProt Q9EQZ5
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