SMTL ID : 7f8p.1 (1 other biounit)

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with new carbapenem drug T203

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 59I: (2R,3R)-3-methyl-4-(2-oxidanylidene-2-propan-2-yloxy-ethyl)sulfanyl-2-[(2R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-2,3-dihydro-1H-pyrrole-5-carboxylic acid(Covalent)

59I.1: 11 residues within 4Å: Chain A: M.265, Y.280, T.282, G.294, H.298, W.302, S.313, H.314, G.315, C.316, N.318 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.280, A:T.282, A:W.302, A:H.314 Hydrogen bonds: A:T.282, A:H.314, A:C.316, A:N.318 Salt bridges: A:H.298

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: A.52, V.53, W.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.53, A:V.53 Water bridges: A:L.67 GOL.4: 4 residues within 4Å: Chain A: E.175, H.176, F.177, I.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.176, A:F.177 Water bridges: A:H.176

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.3: 4 residues within 4Å: Chain A: S.268, P.273, V.274, N.275 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:P.273, A:V.274 Hydrogen bonds: A:S.268, A:S.268, A:V.274, A:N.275 Water bridges: A:S.268, A:S.268

1 x 56X: (4R,5S,6S)-6-((R)-1-hydroxyethyl)-3-((2-isopropoxy-2-oxoethyl)thio)-4-methyl-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid(Non-covalent)

56X.5: 9 residues within 4Å: Chain A: M.119, A.133, R.171, G.257, S.258, Q.289, Y.292, R.333, L.353 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:M.119, A:A.133, A:L.353 Hydrogen bonds: A:S.258, A:Q.289, A:Y.292 Water bridges: A:R.333 Salt bridges: A:R.333, A:R.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, N. et al., Allosteric cooperation in beta-lactam binding to a non-classical transpeptidase. Elife (2022)

Release Date

2022-05-11

Peptides

L,D-transpeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L,D-transpeptidase 2

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