SMTL ID : 8pxz.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x ZGL- JGO- DAL: Peptidoglycan tripeptide(Covalent)

ZGL-JGO-DAL.1: 6 residues within 4Å: Chain A: L.98, M.100, D.122, E.123, R.153, E.187 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.98, A:M.100, A:R.153, A:R.153, A:E.187 Water bridges: A:E.123, A:N.124

1 x ZGL- JGO: Peptidoglycan dipeptide(Non-functional Binders)

ZGL-JGO.2: 13 residues within 4Å: Chain A: Y.265, T.267, S.278, G.279, V.280, H.283, W.287, S.298, H.299, G.300, C.301, N.303 Ligands: DAL.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.265, A:Y.265, A:H.299 Hydrogen bonds: A:T.267, A:H.299, A:H.299, A:H.299, A:C.301, A:N.303 Water bridges: A:Y.265, A:H.299

1 x EDO: 1,2-ETHANEDIOL(Non-covalent)

EDO.3: 1 residues within 4Å: Chain A: Y.277 No protein-ligand interaction detected (PLIP)

1 x DAL: D-ALANINE(Non-covalent)

DAL.4: 3 residues within 4Å: Chain A: T.267, W.287 Ligands: ZGL-JGO.2 No protein-ligand interaction detected (PLIP)

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

CL.5: 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

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