Research workbench
Structure of the light-state dimer of the blue light photoreceptor Aureochrome 1a LOV from P. tricornutum
Analyse Structure of the light-state dimer of the blue light photoreceptor Aureochrome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DKL
- Type
- protein
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Phaeodactylum tricornutum
- Molecule
- LOV domain
- Ligands
- FMN
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LOV domain | protein | 133 | 32% helix, 29% strand | — |
| B | LOV domain | protein | 137 | 34% helix, 29% strand | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.69 | 0.89 | 26 | FMN |
| 2 | 179 | 0.65 | 0.85 | 25 | FMN |
| 3 | 90 | 0.39 | 0.77 | 16 | empty |
| 4 | 89 | 0.39 | 0.76 | 19 | empty |
| 5 | 78 | 0.37 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1633 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 5DKL · Structure of the light-state dimer of the blue light photoreceptor aureochrome 1A lov… · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 5DKL · PDBe 5DKL
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