Research workbench
Dark state structure of the bluf domain of the rhodobacterial protein appa
Analyse Dark state structure of the bluf domain of the rhodobacterial protein appa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IYG
- Type
- protein
- Length
- 217 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Appa, antirepressor of ppsr, sensor of blue light
- UniProt
- Q3J677
- Ligands
- FMN
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Appa, antirepressor of ppsr, sensor of blue light | protein | 109 | 36% helix, 35% strand | Q3J677 |
| B | Appa, antirepressor of ppsr, sensor of blue light | protein | 108 | 35% helix, 37% strand | Q3J677 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.59 | 0.85 | 19 | FMN |
| 2 | 99 | 0.54 | 0.84 | 17 | FMN |
| 3 | 66 | 0.28 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1054 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 2IYG · Dark state structure of the BLUF domain of the rhodobacterial protein AppA · 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
- Every structure of UniProt Q3J677
- Elsewhere: RCSB PDB 2IYG · PDBe 2IYG · UniProt Q3J677
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