Crystallographic superstructure of the photosensory core module (pas- gaf-phy) of the bacterial phytochrome AGP1 (ATBPHP1) locked in a pr- like state

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).

Ligands and binding sites

• JQ2 · 3-[2-[(~{Z})-[12-ethyl-6-(3-hydroxy-3-oxopropyl)-13-methyl-11-oxidanylidene-4,10-diazatricyclo[8.3.0.0^{3, 7}]trideca-1,3,6,12-tetraen-5-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 1650 Ų buried · 8 hydrogen bonds · protein-protein
• C–D · 1643 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 640 Ų buried · 3 hydrogen bonds · protein-protein
• A–D · 225 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 201 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 modified, 4 covalent (engineered, covalent ligand).

Compared structures

• 6R27 · Crystallographic superstructure of the photosensory core module (PAS-GAF-PHY) of the… · 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 Q7CY45
• Elsewhere: RCSB PDB 6R27 · PDBe 6R27 · UniProt Q7CY45