SMTL ID : 6iyw.5 (5 other biounits)

Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with Imipenem adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x IM2: (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid(Covalent)

IM2.1: 8 residues within 4Å: Chain A: M.167, Y.172, Y.182, S.195, G.196, H.216, G.217, C.218 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.182, A:Y.182, A:Y.182, A:H.216, A:C.218

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: E.77, H.78, F.79, I.155, W.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.77, A:F.79 GOL.3: 1 residues within 4Å: Chain A: V.136 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.136 GOL.4: 9 residues within 4Å: Chain A: M.21, E.32, R.73, I.157, V.158, G.159, R.235, G.236, L.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.158, A:R.235, A:G.236 GOL.5: 4 residues within 4Å: Chain A: T.9, S.10, S.11, L.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.9, A:S.10, A:S.11 GOL.6: 4 residues within 4Å: Chain A: G.62, A.63, W.74, R.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.62, A:W.74, A:R.266 Water bridges: A:G.62 GOL.7: 8 residues within 4Å: Chain A: I.54, T.55, T.56, P.59, V.60, E.61, G.62, W.74 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.56, A:T.56, A:G.62 Water bridges: A:E.61, A:E.61, A:E.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, F. et al., The 1-beta-methyl group confers a lower affinity of l,d-transpeptidase LdtMt2 for ertapenem than for imipenem. Biochem. Biophys. Res. Commun. (2019)

Release Date

2019-02-27

Peptides

L,D-transpeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

L,D-transpeptidase 2

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