Far-red absorbing dark state of JSC1_58120G3 with bound biliverdin ixa (bv)

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).

Ligands and binding sites

• BVX · 3-[2-[(~{Z})-[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid · ligand · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 250 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6XHG · Far-red absorbing dark state of JSC1_58120g3 with bound biliverdin IXa (BV) · 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
• Elsewhere: RCSB PDB 6XHG · PDBe 6XHG