Research workbench
The structure of stable-5-lipoxygenase bound to ndga
Analyse The structure of stable-5-lipoxygenase bound to ndga in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N2W
- Type
- protein
- Length
- 1,210 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arachidonate 5-lipoxygenase
- EC
- 1.13.11.34
- UniProt
- P09917
- Ligands
- 30Z, FE2
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arachidonate 5-lipoxygenase (EC 1.13.11.34) | protein | 608 | 43% helix, 15% strand | P09917 |
| B | Arachidonate 5-lipoxygenase (EC 1.13.11.34) | protein | 602 | 44% helix, 14% strand | P09917 |
Ligands and binding sites
- 30Z · 4-[(2R,3S)-3-[(3,4-dihydroxyphenyl)methyl]-2-methylbutyl]benzene-1,2-diol · ligand · chains B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.78 | 0.82 | 74 | empty |
| 2 | 680 | 0.77 | 0.82 | 57 | empty |
| 3 | 564 | 0.77 | 0.83 | 66 | empty |
| 4 | 411 | 0.77 | 0.86 | 62 | empty |
| 5 | 481 | 0.68 | 0.78 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 1136 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6N2W · The structure of Stable-5-Lipoxygenase bound to NDGA · the same entry in another collection · chain A against A, TM-score 1.00
- P09917 · AlphaFold monomer V2.0 prediction for polyunsaturated fatty acid 5-lipoxygenase (P09917) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P09917
- Elsewhere: RCSB PDB 6N2W · PDBe 6N2W · UniProt P09917
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.