SMTL ID : 8a1n.1 (1 other biounit)

Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with fumaryl amide analogue 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x KUS: (Z)-N-(4-chlorophenyl)-4-oxidanylidene-but-2-enamide(Covalent)

KUS.1: 8 residues within 4Å: Chain A: M.250, Y.265, T.267, G.279, W.287, H.299, G.300, C.301 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.265, A:Y.265, A:Y.265, A:T.267, A:W.287 Hydrogen bonds: A:Y.265, A:H.299, A:C.301 Water bridges: A:H.299

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: H.161, F.162, I.238, W.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.162

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

DMS.3: 7 residues within 4Å: Chain A: M.104, E.115, P.116, A.118, E.154, R.156, L.338 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.115 DMS.4: 2 residues within 4Å: Chain A: A.37, V.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.38

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

NA.5: 2 residues within 4Å: Chain A: N.42, Y.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.42, A:Y.71, A:Y.71 NA.6: 4 residues within 4Å: Chain A: I.249, D.251, T.254, Y.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.249, A:D.251

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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