Crystal structure of arabidopsis thaliana phytochrome B photosensory module

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).

Ligands and binding sites

• O6E · 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 11 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A, B
• PGE · Triethylene glycol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 2312 Ų buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 4OUR · Crystal structure of Arabidopsis thaliana phytochrome B photosensory module · the same entry in another collection · chain A against A, TM-score 1.00
• P14713 · AlphaFold monomer V2.0 prediction for phytochrome B (P14713) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 P14713
• Elsewhere: RCSB PDB 4OUR · PDBe 4OUR · UniProt P14713