Research workbench
Crystal structure of P. aeruginosa bacteriophytochrome photosensory core module mutant Q188L in the mixed PR/PFR state
Analyse Crystal structure of P. aeruginosa bacteriophytochrome photosensory core module… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IBR
- Type
- protein
- Length
- 914 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- Q9HWR3
- Ligands
- BLA
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bacteriophytochrome (EC 2.7.13.3) | protein | 457 | 34% helix, 24% strand | Q9HWR3 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.82 | 0.85 | 85 | BLA |
| 2 | 894 | 0.82 | 0.84 | 102 | BLA |
| 3 | 301 | 0.57 | 0.77 | 32 | empty |
| 4 | 265 | 0.48 | 0.73 | 35 | empty |
| 5 | 79 | 0.40 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1537 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified, 2 cofactor (engineered, biliverdin attachment).
Compared structures
- 3IBR · Crystal Structure of P. aeruginosa Bacteriophytochrome Photosensory Core Module Mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HWR3 · AlphaFold monomer V2.0 prediction for bacteriophytochrome (Q9HWR3) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9HWR3
- Elsewhere: RCSB PDB 3IBR · PDBe 3IBR · UniProt Q9HWR3
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