MolNFT v2 · #116957 · protein
Structure of the dark-state monomer of the blue light photoreceptor Aureochrome 1a LOV from P. tricornutum
5DKK · LOV domain: “Structure of the dark-state monomer of the blue light photoreceptor Aureochrome 1a LOV from P. tricornutum”. X-ray diffraction at 2.5, 1 ligand (FMN), 4 pockets (best druggability 0.75). MolNFT v2 #116957 on GenesisL1…
- PDB
- 5DKK
- Type
- protein
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Phaeodactylum tricornutum
- Molecule
- LOV domain
- Ligands
- FMN
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 40% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LOV domain | protein | 134 | 40% helix, 30% strand | — |
| B | LOV domain | protein | 136 | 40% helix, 29% strand | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.75 | 0.80 | 64 | empty |
| 2 | 164 | 0.67 | 0.87 | 23 | FMN |
| 3 | 151 | 0.64 | 0.86 | 23 | FMN |
| 4 | 339 | 0.60 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 838 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5DKK · Structure of the dark-state monomer 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 5DKK · PDBe 5DKK
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