Research workbench
Crystal structure of anti-configuration of indomethacin and leukotriene B4 12-HYDROXYDEHYDROGENASE/15-oxo-prostaglandin 13- reductase complex
Analyse Crystal structure of anti-configuration of indomethacin and leukotriene B4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DM6
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-dependent leukotriene B4 12-hydroxydehydrogenase
- EC
- 1.3.1.74, 1.3.1.48
- UniProt
- Q9EQZ5
- Ligands
- NAP, IMN, TAM
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADP-dependent leukotriene B4 12-hydroxydehydrogenase (EC 1.3.1.74, 1.3.1.48) | protein | 331 | 31% helix, 27% strand | Q9EQZ5 |
| B | NADP-dependent leukotriene B4 12-hydroxydehydrogenase (EC 1.3.1.74, 1.3.1.48) | protein | 333 | 32% helix, 26% strand | Q9EQZ5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- IMN · Indomethacin · ligand · chains A, B
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.82 | 0.97 | 38 | empty |
| 2 | 571 | 0.81 | 0.86 | 60 | NAP |
| 3 | 713 | 0.80 | 0.84 | 72 | NAP, IMN |
| 4 | 88 | 0.52 | 0.84 | 29 | empty |
| 5 | 76 | 0.48 | 0.83 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1189 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2DM6 · Crystal structure of anti-configuration of indomethacin and leukotriene B4… · 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 2DM6 · PDBe 2DM6 · UniProt Q9EQZ5
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