Research workbench
Structure of a parallel dimer of the aureochrome 1a LOV domain from Phaeodactylum tricornutum
Analyse Structure of a parallel dimer of the aureochrome 1a LOV domain from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A8B
- Type
- protein
- Length
- 533 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.791
- Source
- PHAEODACTYLUM TRICORNUTUM
- Molecule
- PTAUREO1A LOV2 domain
- Ligands
- FMN, CL
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.791 · 3 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PTAUREO1A LOV2 domain | protein | 132 | 38% helix, 30% strand | — |
| B, D | PTAUREO1A LOV2 domain | protein | 131 | 36% helix, 30% strand | — |
| C | PTAUREO1A LOV2 domain | protein | 139 | 37% helix, 28% strand | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.82 | 0.83 | 92 | FMN |
| 2 | 740 | 0.78 | 0.82 | 52 | CL, GOL |
| 3 | 516 | 0.72 | 0.80 | 49 | CL |
| 4 | 167 | 0.70 | 0.89 | 22 | FMN |
| 5 | 150 | 0.67 | 0.87 | 21 | FMN |
Interfaces
3 interfaces between chains.
- A–B · 1027 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 967 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 536 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5A8B · Structure of a parallel dimer of the aureochrome 1A lov domain from phaeodactylum… · 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 5A8B · PDBe 5A8B
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