MolNFT v1 · #61861 · protein
Allene oxide synthase 8R-lipoxygenase from plexaura homomalla
3DY5 · Allene oxide synthase-lipoxygenase protein: “Allene oxide synthase 8R-lipoxygenase from plexaura homomalla”. X-ray diffraction, 2 ligands (HEM, FE2), 20 pockets (best druggability 0.84). MolNFT v1 #61861 on GenesisL1: 3D structure…
- PDB
- 3DY5
- Type
- protein
- Length
- 2,004 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allene oxide synthase-lipoxygenase protein
- EC
- 4.2.1.92, 1.13.11.40
- UniProt
- O16025
- Ligands
- HEM, FE2
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Allene oxide synthase-lipoxygenase protein (EC 4.2.1.92, 1.13.11.40) | protein | 1002 | 35% helix, 15% strand | O16025 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C
- FE2 · Fe (II) ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.84 | 0.89 | 60 | HEM |
| 2 | 550 | 0.84 | 0.89 | 57 | HEM |
| 3 | 640 | 0.81 | 0.85 | 85 | empty |
| 4 | 424 | 0.78 | 0.87 | 59 | empty |
| 5 | 900 | 0.77 | 0.80 | 90 | empty |
Interfaces
1 interface between chains.
- A–C · 496 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3DY5 · Allene oxide synthase 8R-lipoxygenase from Plexaura homomalla · the same entry in another collection · chain A against A, TM-score 1.00
- O16025 · AlphaFold monomer V2.0 prediction for allene oxide synthase- lipoxygenase protein (O16025) · a predicted model of the same protein · chain C 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 O16025
- Elsewhere: RCSB PDB 3DY5 · PDBe 3DY5 · UniProt O16025
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