Research workbench
Crystal structure of leukotriene B4 12- HYDROXYDEHYDROGENASE/15-oxo-prostaglandin 13-reductase complexed with NADP and 15-oxo-PGE2
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
- 1V3V
- Type
- protein
- Length
- 661 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
- NAP, 5OP, CL
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leukotriene B4 12- HYDROXYDEHYDROGENASE/PROSTAGLANDIN 15-keto reductase (EC 1.3.1.48) | protein | 333 | 33% helix, 26% strand | Q9EQZ5 |
| B | Leukotriene B4 12- HYDROXYDEHYDROGENASE/PROSTAGLANDIN 15-keto reductase (EC 1.3.1.48) | protein | 328 | 33% helix, 27% strand | Q9EQZ5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 5OP · (5E,13E)-11-hydroxy-9,15-dioxoprosta-5,13-dien-1-oic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 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 | 181 | 0.83 | 0.97 | 42 | empty |
| 2 | 533 | 0.80 | 0.86 | 58 | NAP, 5OP |
| 3 | 560 | 0.79 | 0.85 | 60 | NAP, 5OP |
| 4 | 55 | 0.47 | 0.85 | 22 | empty |
| 5 | 50 | 0.26 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1232 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1V3V · 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 B 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 Q9EQZ5
- Elsewhere: RCSB PDB 1V3V · PDBe 1V3V · UniProt Q9EQZ5
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