› 5duj

X-ray diffraction
2.17Å resolution

Crystal structure of ldtMt2 in complex with Faropenem adduct

Released:
DOI: 10.2210/pdb5duj/pdb
PDB entry 5duj coloured by chain, front view.
PDB entry 5duj coloured by chain, side view.
PDB entry 5duj coloured by chain, top view.
Source organism: Mycobacterium tuberculosis CDC1551
Primary publication:
Non-classical transpeptidases yield insight into new antibacterials.
Kumar P, Kaushik A, Lloyd EP, Li SG, Mattoo R, Ammerman NC, Bell DT, Perryman AL, Zandi TA, Ekins S, Ginell SL, Townsend CA, Freundlich JS, Lamichhane G
OpenAccess logo Nat Chem Biol 13 54-61 (2017)
PMID: 27820797

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-125201 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L,D-transpeptidase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 370 amino acids
Theoretical weight: 39.53 KDa
Source organism: Mycobacterium tuberculosis CDC1551
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: I6Y9J2 (Residues: 42-408; Coverage: 98%)
Gene names: P425_02624, RVBD_2518c, Rv2518c, ldtB, lppS
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 1 x SO4
Ligand BME 2 x BME
Ligand DGF 2 x DGF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 61.051Å b: 93.929Å c: 75.215Å
α: 90° β: 92.72° γ: 90°
R-values:
R R work R free
0.183 0.18 0.234
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

Mycobacterium abscessus and β-Lactams: Emerging Insights and Potential Opportunities.
Story-Roller et al. (2018)
7 more

2 mentions without citation

Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan.
Vermassen et al. (2019)
1 more