SMTL ID : 6boi.2 (1 other biounit)

Crystal Structure of LdtMt2 (56-408) with a panipenem adduct at the active site cysteine-354

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x E0Y: (3S,5R)-5-[(2R,3R)-1,3-dihydroxybutan-2-yl]-3-({(3R)-1-[(1E)-ethanimidoyl]pyrrolidin-3-yl}sulfanyl)-L-proline(Covalent)

E0Y.1: 11 residues within 4Å: Chain A: M.248, Y.263, T.265, G.277, H.281, W.285, S.296, H.297, G.298, C.299, N.301 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:M.248, A:Y.263, A:W.285 Hydrogen bonds: A:H.297, A:C.299, A:N.301 Water bridges: A:G.277, A:H.297 Salt bridges: A:H.281, A:H.297

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: S.251, P.256, V.257, N.258 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.251, A:V.257, A:N.258, A:N.258 PEG.3: 6 residues within 4Å: Chain A: I.236, W.339, N.340, I.341, P.342, W.343 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: L.330, P.331, G.332, I.333, N.340, I.341, P.342, Q.345 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.332, A:I.333, A:N.340 GOL.5: 6 residues within 4Å: Chain A: I.133, K.134, I.135, G.143, F.145, W.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.133, A:I.135

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain A: R.242, R.316 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.242 Salt bridges: A:R.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saavedra, H. et al., Structures and Mechanism of Inhibition of Mycobacterium tuberculosis L,D-transpeptidase 2 by Panipenem. To Be Published

Release Date

2018-04-11

Peptides

Putative conserved lipoprotein LppS: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Putative conserved lipoprotein LppS

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