› 5e1g

X-ray diffraction
1.85Å resolution

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T208

Released:
DOI: 10.2210/pdb5e1g/pdb
PDB entry 5e1g coloured by chain, front view.
PDB entry 5e1g coloured by chain, side view.
PDB entry 5e1g coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
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 H37Rv
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

1 bound ligand:
Ligand T8G 1 x T8G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 61.283Å b: 93.872Å c: 75.358Å
α: 90° β: 93.08° γ: 90°
R-values:
R R work R free
0.198 0.197 0.227
Expression system: Escherichia coli BL21(DE3)

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Citations

9 review citations

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

2 mentions without citation

Non-classical transpeptidases yield insight into new antibacterials.
Kumar et al. (2017)
1 more