Crystal structure of pseudomonas aeruginosa D-arginine dehydrogenase Y249F co-crystallized in the presence of D-arginine

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).

Ligands and binding sites

• 4R2 · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(~{E})-4-carbamimidamidobut-2-enoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3, 4-tris(oxidanyl)pentyl] hydrogen phosphate · ligand · chains A
• 6FA · 6-hydroxy-flavin-adenine dinucleotide · ligand · chains A
• GOL · Glycerol · additive · 3 copies · chains A
• PEG · Di(hydroxyethyl)ether · 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, 1 with a druggability of 0.5 or more.

Compared structures

• 7RDF · Crystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9HXE3 · AlphaFold monomer V2.0 prediction for FAD-dependent catabolic D-arginine dehydrogenase… · a predicted model of the same protein · 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 Q9HXE3
• Elsewhere: RCSB PDB 7RDF · PDBe 7RDF · UniProt Q9HXE3