Research workbench
Crystal structure of the dark-adapted full-length bacteriophytochrome xccbphp from xanthomonas campestris in the pr state bound to bv chromophore
Analyse Crystal structure of the dark-adapted full-length bacteriophytochrome xccbphp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PL0
- Type
- protein
- Length
- 1,214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- UniProt
- A0A0H2XCS3
- Ligands
- BLA
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome | protein | 606 | 33% helix, 25% strand | A0A0H2XCS3 |
| B | Bacteriophytochrome | protein | 608 | 33% helix, 26% strand | A0A0H2XCS3 |
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
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.81 | 0.91 | 41 | BLA |
| 2 | 320 | 0.80 | 0.90 | 36 | BLA |
| 3 | 578 | 0.78 | 0.84 | 77 | empty |
| 4 | 382 | 0.74 | 0.85 | 36 | empty |
| 5 | 481 | 0.73 | 0.82 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 3402 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 6PL0 · Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP from… · 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 6PL0 · PDBe 6PL0 · UniProt A0A0H2XCS3
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