Structural basis for the inhibition of mycobacterium tuberculosis L,D- transpeptidase by meropenem, a drug effective against extensively drug-resistant strains

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 40% strand (DSSP).

Ligands and binding sites

• DWZ · (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1408 Ų buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 4GSU · Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by… · the same entry in another collection · chain A against A, TM-score 1.00
• O53223 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (O53223) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 O53223
• Elsewhere: RCSB PDB 4GSU · PDBe 4GSU · UniProt O53223