Research workbench
Crystal structure of the chromophore-binding domain of stigmatella aurantiaca bacteriophytochrome (THR289HIS mutant) in the pr state
Analyse Crystal structure of the chromophore-binding domain of stigmatella aurantiaca… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RQ9
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photoreceptor-histidine kinase bphp
- UniProt
- Q097N3
- Ligands
- BLA, SRT
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photoreceptor-histidine kinase bphp | protein | 304 | 34% helix, 29% strand | Q097N3 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · chains A
- SRT · S,R meso-tartaric acid · ligand · chains A
- GOL · Glycerol · additive · 15 copies · chains A
- 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.76 | 0.89 | 33 | BLA |
| 2 | 315 | 0.60 | 0.78 | 28 | GOL |
| 3 | 153 | 0.47 | 0.77 | 21 | GOL |
| 4 | 66 | 0.44 | 0.82 | 13 | empty |
Modifications
Observed in the structure: 1 cofactor (biliverdin attachment).
Compared structures
- 4RQ9 · Crystal structure of the chromophore-binding domain of Stigmatella aurantiaca… · 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 Q097N3
- Elsewhere: RCSB PDB 4RQ9 · PDBe 4RQ9 · UniProt Q097N3
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