Structure and specificity of L-D-transpeptidase from mycobacterium tuberculosis and antibiotic resistance: calcium binding promotes dimer formation

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 42% strand (DSSP).

Ligands and binding sites

• MLD · Glcnac(beta1-4)-murnac(1,6-anhydro)-L-ala-gamma-D-glu-meso-A2PM-D-ala · ligand · chains A
• 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 · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Modifications

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

Compared structures

• 4QR7 · Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and… · the same entry in another collection · chain A against A, TM-score 1.00
• I6Y9J2 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (I6Y9J2) · 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 I6Y9J2
• Elsewhere: RCSB PDB 4QR7 · PDBe 4QR7 · UniProt I6Y9J2