Research workbench
Structure of a light-induced intermediate of the bluf domain of the rhodobacterial protein appa
Analyse Structure of a light-induced intermediate of the bluf domain of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IYI
- Type
- protein
- Length
- 214 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 0.58
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Appa, antirepressor of ppsr, sensor of blue light | protein | 108 | 35% helix, 36% strand | Q3J677 |
| B | Appa, antirepressor of ppsr, sensor of blue light | protein | 106 | 36% 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 | 106 | 0.58 | 0.85 | 17 | FMN |
| 2 | 106 | 0.54 | 0.83 | 17 | FMN |
| 3 | 62 | 0.27 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1067 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 2IYI · structure of a light-induced intermediate of the BLUF domain of the rhodobacterial… · 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 2IYI · PDBe 2IYI · UniProt Q3J677
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