SMTL ID : 8bk3.1

Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with diepoxide ketone 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

1 x QXU: 1-[(2~{S},3~{R})-3-phenyloxiran-2-yl]ethanone(Covalent)

QXU.1: 11 residues within 4Å: Chain A: M.250, Y.265, T.267, G.279, H.283, W.287, S.298, H.299, G.300, C.301 Ligands: NO3.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.265, A:Y.265, A:T.267, A:W.287 Hydrogen bonds: A:H.299, A:H.299, A:C.301 Water bridges: A:N.303

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 8 residues within 4Å: Chain A: Y.265, S.278, G.279, V.280, H.299, G.300, C.301 Ligands: QXU.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.278, A:H.299 Water bridges: A:Y.265, A:S.278 NO3.3: 6 residues within 4Å: Chain A: M.104, E.115, P.116, A.118, R.156, L.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.116 Water bridges: A:R.318 NO3.4: 4 residues within 4Å: Chain A: N.42, R.46, E.63, Y.71 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.42, A:Q.64, A:Y.71 Water bridges: A:R.69 NO3.7: 5 residues within 4Å: Chain B: N.42, E.63, Q.64, G.66, Y.71 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.42, B:E.63, B:G.66, B:Y.71, B:Y.71 Water bridges: B:R.69

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: G.256, V.257, P.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.256

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

EDO.6: 3 residues within 4Å: Chain A: H.161, F.162, W.341 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.161, A:F.162

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

DMS.8: 4 residues within 4Å: Chain B: D.43, N.68, R.69, R.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.70 Salt bridges: B:D.43 DMS.9: 6 residues within 4Å: Chain B: M.104, E.115, P.116, A.118, R.156, L.338 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Munnik, M. et al., alpha beta , alpha ' beta '-Diepoxyketones are mechanism-based inhibitors of nucleophilic cysteine enzymes. Chem.Commun.(Camb.) (2023)

Release Date

2023-11-22

Peptides

L,D-transpeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L,D-transpeptidase 2

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