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

A third intermediate state of L,D-transpeptidase LdtMt2-ertapenem adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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: 8 residues within 4Å: Chain A: M.164, Y.169, Y.179, S.192, G.193, H.213, G.214, C.215 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.164 Hydrogen bonds: A:Y.179, A:Y.179, A:H.213, A:C.215 Salt bridges: A:H.213

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: I.49, K.50, I.51, G.59, F.61, W.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.49, A:I.51 Water bridges: A:G.59 GOL.3: 5 residues within 4Å: Chain A: E.74, H.75, F.76, I.152, W.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.75, A:F.76 GOL.4: 5 residues within 4Å: Chain A: K.160, W.185, Q.224, Y.227, D.228 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.160, A:Q.224, A:D.228, A:D.228 Water bridges: A:D.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X.Y. et al., A New State I-plus Observed for the L,D-transpeptidase LdtMt2-ertapenem Adduct. Prog.Biochem.Biophys. (2020)

Release Date

2021-01-13

Peptides

L,D-transpeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L,D-transpeptidase 2

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