› 5dcc

X-ray diffraction
2.45Å resolution

X-RAY CRYSTAL STRUCTURE OF a TEBIPENEM ADDUCT OF L,D TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS

Released:
DOI: 10.2210/pdb5dcc/pdb
PDB entry 5dcc coloured by chain, front view.
PDB entry 5dcc coloured by chain, side view.
PDB entry 5dcc coloured by chain, top view.
Source organism: Mycobacterium tuberculosis CDC1551
Primary publication:
Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase LdtMt2 by biapenem and tebipenem.
Bianchet MA, Pan YH, Basta LAB, Saavedra H, Lloyd EP, Kumar P, Mattoo R, Townsend CA, Lamichhane G
OpenAccess logo BMC Biochem 18 8 (2017)
PMID: 28545389

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
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: 353 amino acids
Theoretical weight: 37.79 KDa
Source organism: Mycobacterium tuberculosis CDC1551
Expression system: Escherichia coli
UniProt:
  • Canonical: I6Y9J2 (Residues: 56-408; Coverage: 94%)
Gene names: P425_02624, RVBD_2518c, Rv2518c, ldtB, lppS
Sequence domains:
Structure domains:

Ligands and Environments

6 bound ligands:
Ligand 58U 2 x 58U
Ligand SO4 9 x SO4
Ligand PEG 9 x PEG
Ligand PGE 7 x PGE
Ligand GOL 4 x GOL
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 60.934Å b: 94.4Å c: 75.385Å
α: 90° β: 92.88° γ: 90°
R-values:
R R work R free
0.173 0.168 0.214
Expression system: Escherichia coli

Quick links

Citations

6 review citations

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

1 mention without citation

Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase LdtMt2 by biapenem and tebipenem.
Bianchet et al. (2017)