SMTL ID : 6iyv.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x 2RG: (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid(Covalent)

2RG.1: 10 residues within 4Å: Chain A: M.167, Y.172, V.174, Y.182, S.195, G.196, H.216, G.217, C.218 Ligands: GOL.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.174 Hydrogen bonds: A:Y.172, A:Y.182, A:Y.182, A:C.218 Water bridges: A:D.168, A:H.216 Salt bridges: A:H.216

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.115, V.117, H.232, K.234 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.115, A:D.115, A:H.232, A:K.234 Water bridges: A:K.234, A:K.234 GOL.3: 5 residues within 4Å: Chain A: E.77, H.78, F.79, I.155, W.258 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.77, A:H.78, A:F.79 Water bridges: A:W.258 GOL.4: 2 residues within 4Å: Chain A: P.82, D.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.115 GOL.5: 6 residues within 4Å: Chain A: R.161, Y.230, D.231, H.232, V.233, K.234 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.233 Water bridges: A:K.234, A:K.234, A:K.234 GOL.6: 1 residues within 4Å: Ligands: 2RG.1 No protein-ligand interaction detected (PLIP)

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

PEG.7: 7 residues within 4Å: Chain A: G.25, A.85, V.86, D.87, H.110, F.111, T.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.87 PEG.8: 3 residues within 4Å: Chain A: T.56, N.57, D.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.87

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

SO4.9: 2 residues within 4Å: Chain A: T.184, W.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.184

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 LdtMt2for 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
B

L,D-transpeptidase 2

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