Crystal structure of the RU(BPY)2PHENA functionalized P450 BM3 L407C heme domain mutant in complex with N-palmitoylglycine

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 11% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
• 140 · N-palmitoylglycine · ligand · 2 copies · chains A, B
• RU8 · bis(2,2'-bipyridine-kappa~2~N~1~,N~1'~)[2-iodo-N-(1,10-phenanthrolin-5-yl-kappa~2~N~1~,N~10~)acetamide]ruthenium(2+) · ligand · 2 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1050 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 5JQ2 · Crystal structure of the Ru(bpy)2PhenA functionalized P450 BM3 L407C heme domain mutant… · the same entry in another collection · chain A against A, TM-score 1.00
• P14779 · AlphaFold monomer V2.0 prediction for bifunctional cytochrome P450/NADPH--P450 reductase… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P14779
• Elsewhere: RCSB PDB 5JQ2 · PDBe 5JQ2 · UniProt P14779