Crystal structure of udp-N-acetylmuramoylalanine--D-glutamate ligase (murd) from pseudomonas aeruginosa PAO1 in complex with uma (uridine- 5'-diphosphate-N-acetylmuramoyl-L-alanine)

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).

Ligands and binding sites

• UMA · Uridine-5'-diphosphate-N-acetylmuramoyl-L-alanine · ligand · chains A
• MG · Magnesium ion · metal · chains A
• PO4 · Phosphate ion · ion · chains A
• GOL · Glycerol · additive · 2 copies · chains A
• PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains A
• SIN · Succinic acid · additive · chains A
• ACT · Acetate ion · 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, 2 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 1 modified (carboxylation).

Compared structures

• 8DP2 · Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9HVZ9 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramoylalanine-- D-glutamate ligase… · 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 Q9HVZ9
• Elsewhere: RCSB PDB 8DP2 · PDBe 8DP2 · UniProt Q9HVZ9