SMTL ID : 8pxy.1

Crystal structure of the transpeptidase LdtMt2 C354S mutant from Mycobacterium tuberculosis in complex with natural substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x ALA- ZGL- JGO- DAL: Peptidoglycan tetrapeptide(Non-covalent)

ALA-ZGL-JGO-DAL.1: 9 residues within 4Å: Chain A: L.98, T.99, M.100, R.120, D.122, E.123, R.153, E.187 Ligands: MUB-NAG.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:D.122 Hydrogen bonds: A:M.100, A:D.122, A:E.123, A:E.123, A:R.153, A:R.153, A:E.187 Water bridges: A:H.97, A:H.97, A:R.120, A:R.120, A:R.120, A:E.123 Salt bridges: A:R.120, A:R.153

1 x MUB- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid(Non-functional Binders)

MUB-NAG.2: 2 residues within 4Å: Ligands: ALA-ZGL-JGO-DAL.1, ALA-ZGL-JGO-DAL.1 No protein-ligand interaction detected (PLIP)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 4 residues within 4Å: Chain A: T.267, W.287, T.297, H.299 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.299

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: N.42, N.44, R.46, R.69 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Munnik, M. et al., Biochemical and crystallographic studies of L,D-transpeptidase 2 from Mycobacterium tuberculosis with its natural monomer substrate. Commun Biol (2024)

Release Date

2024-08-07

Peptides

L,D-transpeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L,D-transpeptidase 2