Structure of S. aureus rel catalytic domains in complex with pppgpp

Structure

x-ray diffraction · 2 distinct chains · 63% helix, 10% strand (DSSP).

Ligands and binding sites

• C1Z · Guanosine 3'-diphosphate 5'-triphosphate · ligand · 4 copies · chains A, B
• VF5 · [[(3~{A}~{R},4~{R},6~{R},6~{A}~{R})-4-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-2-oxidanyl-2-oxidanylidene-3~{A},4,6,6~{A}-tetrahydrofuro[3,4-D][1, 3,2]dioxaphosphol-6-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A
• MG · Magnesium ion · metal · 3 copies · chains A
• MN · Manganese (II) ion · metal · 2 copies · chains A, B
• IOD · Iodide ion · ion · 12 copies · chains A, B
• GOL · Glycerol · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 890 Ų buried · 11 hydrogen bonds · protein-protein

Compared structures

• 7OIW · Structure of S. aureus Rel catalytic domains in complex with pppGpp · the same entry in another collection · chain A against A, TM-score 1.00
• Q931Q4 · AlphaFold monomer V2.0 prediction for GTP pyrophosphokinase (Q931Q4) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q931Q4
• Elsewhere: RCSB PDB 7OIW · PDBe 7OIW · UniProt Q931Q4