› 8aho

X-ray diffraction
2.3Å resolution

Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with cyanamide analogue 31

Released:
DOI: 10.2210/pdb8aho/pdb
PDB entry 8aho coloured by chain, front view.
PDB entry 8aho coloured by chain, side view.
PDB entry 8aho coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
High-throughput screen with the l,d-transpeptidase LdtMt2 of Mycobacterium tuberculosis reveals novel classes of covalently reacting inhibitors.
de Munnik M, Lang PA, De Dios Anton F, Cacho M, Bates RH, Brem J, Rodríguez Miquel B, Schofield CJ
OpenAccess logo Chem Sci 14 7262-7278 (2023)
PMID: 37416715

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

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: 355 amino acids
Theoretical weight: 38.05 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: I6Y9J2 (Residues: 56-408; Coverage: 94%)
Gene names: P425_02624, RVBD_2518c, Rv2518c, ldtB, lppS
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand NO3 2 x NO3
Ligand DMS 6 x DMS
Ligand NA 2 x NA
Ligand CL 1 x CL
1 modified residue:
Ligand QCS 2 x QCS

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 61.25Å b: 94.261Å c: 75.667Å
α: 90° β: 92.69° γ: 90°
R-values:
R R work R free
0.211 0.209 0.248
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

αβ,α'β'-Diepoxyketones are mechanism-based inhibitors of nucleophilic cysteine enzymes.
de Munnik et al. (2023)

1 mention without citation

High-throughput screen with the l,d-transpeptidase LdtMt2 of Mycobacterium tuberculosis reveals novel classes of covalently reacting inhibitors.
de Munnik et al. (2023)