SMTL ID : 7onn.1

Crystal structure of PBP3 transpeptidase domain from E. coli in complex with AIC499

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x VL5: (2S)-2-[(Z)-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2S)-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[N-[(3R)-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic acid(Covalent)

VL5.1: 20 residues within 4Å: Chain A: E.144, G.146, S.147, K.150, V.184, S.199, N.201, F.257, G.258, Y.259, K.334, T.335, G.336, T.337, A.338, K.339, Y.347, Y.380, Y.381 Ligands: 12P.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.184, A:Y.381 Hydrogen bonds: A:E.144, A:S.147, A:S.199, A:N.201, A:Y.259, A:Y.259, A:T.337, A:T.337, A:T.337, A:K.339 Water bridges: A:T.335, A:G.383 Salt bridges: A:K.334 pi-Stacking: A:Y.259, A:Y.380

2 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.2: 2 residues within 4Å: Chain A: S.3, E.25 No protein-ligand interaction detected (PLIP) 12P.3: 11 residues within 4Å: Chain A: E.180, I.181, K.182, N.201, K.244, W.247, E.251, T.254, Y.259, G.260 Ligands: VL5.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.201, A:T.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freischem, S. et al., Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria. Biomolecules (2021)

Release Date

2021-08-04

Peptides

Peptidoglycan D,D-transpeptidase FtsI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptidoglycan D,D-transpeptidase FtsI

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