Crystal sturucture of L,D-transpeptidase LDTMT2 from mycobacterium tuberculosis in complex with ertapenem adduct

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 39% strand (DSSP).

Ligands and binding sites

• 2RG · (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl) carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains B, A
• SO4 · Sulfate ion · ion · chains B
• GOL · Glycerol · additive · 10 copies · chains B, A
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, A
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• B–A · 542 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 6IYV · Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in… · 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 0.97

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 I6Y9J2
• Elsewhere: RCSB PDB 6IYV · PDBe 6IYV · UniProt I6Y9J2