Research workbench
Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP-G454E variant from Xanthomonas campestris in the Pfr state
Analyse Crystal structure of the dark-adapted full-length bacteriophytochrome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L59
- Type
- protein
- Length
- 600 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.68
- Source
- Xanthomonas campestris pv. campestris (strain 8004)
- Molecule
- Bacteriophytochrome
- UniProt
- A0A0H2XCS3
- Ligands
- BLA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.68 · 1 distinct chain · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome | protein | 600 | 34% helix, 22% strand | A0A0H2XCS3 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.80 | 0.89 | 44 | BLA |
| 2 | 412 | 0.58 | 0.75 | 43 | empty |
| 3 | 218 | 0.57 | 0.79 | 19 | empty |
| 4 | 167 | 0.48 | 0.77 | 19 | empty |
| 5 | 63 | 0.43 | 0.82 | 17 | empty |
Modifications
Observed in the structure: 1 cofactor (biliverdin attachment).
Compared structures
- 7L59 · Crystal structure of the dark-adapted full-length bacteriophytochrome xccbphp-G454E… · 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 A0A0H2XCS3
- Elsewhere: RCSB PDB 7L59 · PDBe 7L59 · UniProt A0A0H2XCS3
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