MolNFT v1 · #40633 · protein
Dark state structure of the bluf domain of the rhodobacterial protein appa
2IYG · Appa, antirepressor of ppsr, sensor of blue light: “Dark state structure of the bluf domain of the rhodobacterial protein appa”. X-ray diffraction, 1 ligand (FMN), 3 pockets (best druggability 0.59). MolNFT v1 #40633 on GenesisL1…
- 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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