SMTL ID : 8a1o.1

Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with acrylamide analogue 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 6 residues within 4Å: Chain A: M.104, E.115, P.116, A.118, R.156, L.338 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.115

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: N.151, N.152 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.152, A:N.152 Water bridges: A:N.124, A:R.128

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: N.44, G.45 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.46

1 x KTI: (E)-3-chloranyl-3-[(2-chlorophenyl)methylsulfonyl]-N-(5-methoxypyridin-2-yl)prop-2-enamide(Covalent)

KTI.4: 13 residues within 4Å: Chain A: M.250, Y.265, V.269, G.279, F.281, H.283, W.287, T.297, S.298, H.299, G.300, C.301, N.303 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.265, A:V.269, A:W.287, A:W.287 Hydrogen bonds: A:H.283, A:H.299, A:C.301, A:N.303 pi-Stacking: A:H.299

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: N.68, R.70 No protein-ligand interaction detected (PLIP)

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

CL.6: 2 residues within 4Å: Chain A: G.279, H.299 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: F.281 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Munnik, M. et al., High-throughput screen with the l,d-transpeptidase Ldt Mt2 of Mycobacterium tuberculosis reveals novel classes of covalently reacting inhibitors. Chem Sci (2023)

Release Date

2023-06-14

Peptides

L,D-transpeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L,D-transpeptidase 2

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