Crystal structure of the D97N variant of dinitrogenase reductase-activating glycohydrolase (drag) from rhodospirillum rubrum in complex with ADP-ribose

Structure

x-ray diffraction · 1 distinct chain · 66% helix, 3% strand (DSSP).

Ligands and binding sites

• AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 3 copies · chains A, C, B
• MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
• TLA · L(+)-tartaric acid · additive · chains A
• GOL · Glycerol · additive · chains A

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–C · 768 Ų buried · 10 hydrogen bonds · protein-protein
• B–C · 545 Ų buried · 4 hydrogen bonds · protein-protein
• A–B · 267 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 2WOE · Crystal Structure of the D97N variant of dinitrogenase reductase- activating… · the same entry in another collection · chain A against A, TM-score 1.00
• P14300 · AlphaFold monomer V2.0 prediction for ADP-ribosyl-[dinitrogen reductase] glycohydrolase… · a predicted model of the same protein · chain C 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 P14300
• Elsewhere: RCSB PDB 2WOE · PDBe 2WOE · UniProt P14300