Chromophore binding domain of bacteriophytochrome linked diguanylyl cyclase from idiomarina species A28L (dimeric pfr-like state).

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).

Ligands and binding sites

• LBV · 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid · ligand · 8 copies · chains A, B, C, D, G, E, F, H
• CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Interfaces

15 interfaces between chains.

• A–D · 1498 Ų buried · 9 hydrogen bonds · protein-protein
• B–F · 1429 Ų buried · 10 hydrogen bonds · protein-protein
• F–H · 924 Ų buried · 7 hydrogen bonds · protein-protein
• D–G · 897 Ų buried · 6 hydrogen bonds · protein-protein
• A–F · 512 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (biliverdin attachment).

Compared structures

• 6SAW · Chromophore binding domain of bacteriophytochrome linked diguanylyl cyclase 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 F7RW09
• Elsewhere: RCSB PDB 6SAW · PDBe 6SAW · UniProt F7RW09