Research workbench
Lipoxygenase-3 (soybean) complex with 13(S)-hydroperoxy-9(Z),11(E)- octadecadienoic acid
Analyse Lipoxygenase-3 (soybean) complex with 13(S)-hydroperoxy-9(Z),11(E)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IK3
- Type
- protein
- Length
- 836 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoxygenase-3
- EC
- 1.13.11.12
- UniProt
- P09186
- Ligands
- 13S, 13R, 9OH, 11O, FE
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoxygenase-3 (EC 1.13.11.12) | protein | 836 | 38% helix, 14% strand | P09186 |
Ligands and binding sites
- 13S · 13(S)-hydroperoxy-9(Z),11(E)-octadecadienoic acid · ligand · chains A
- 13R · 13(R)-hydroperoxy-9(Z),11(E)-octadecadienoic acid · ligand · chains A
- 9OH · (trans-12,13-epoxy)-9-hydroxy-10(E)-octadecenoic acid · ligand · chains A
- 11O · (trans-12,13-epoxy)-11-hydroxy-9(Z)-octadecenoic acid · ligand · chains A
- FE · Fe (III) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.81 | 0.87 | 56 | empty |
| 2 | 101 | 0.77 | 0.97 | 27 | 13S, 13R, 9OH, 11O |
| 3 | 54 | 0.72 | 0.99 | 22 | empty |
| 4 | 549 | 0.72 | 0.80 | 43 | empty |
| 5 | 430 | 0.71 | 0.82 | 48 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1IK3 · Lipoxygenase-3 (soybean) complex with 13(S)-hydroperoxy-9(Z),11(E)-octadecadienoic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P09186 · AlphaFold monomer V2.0 prediction for seed linoleate 9S-lipoxygenase-3 (P09186) · a predicted model of the same protein · chain A 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 P09186
- Elsewhere: RCSB PDB 1IK3 · PDBe 1IK3 · UniProt P09186
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