SMTL ID : 7onw.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 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: 19 residues within 4Å: Chain A: E.280, G.282, S.283, K.286, V.320, S.335, N.337, F.393, G.394, Y.395, T.471, G.472, T.473, A.474, K.475, Y.483, Y.517, G.518 Ligands: MPD.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.320, A:V.320, A:T.473, A:Y.517 Hydrogen bonds: A:S.283, A:S.335, A:N.337, A:Y.395, A:T.471, A:T.473, A:T.473, A:T.473, A:T.473, A:K.475, A:K.475, A:G.518, A:G.519 Salt bridges: A:K.475 pi-Stacking: A:Y.395

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: R.373, S.374 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.374, A:S.374 Salt bridges: A:R.373 PO4.3: 2 residues within 4Å: Chain A: Q.381, R.382 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.381, A:Q.381

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 2 residues within 4Å: Chain A: A.227, P.524 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.227, A:P.524 MPD.5: 6 residues within 4Å: Chain A: G.456, K.459, Y.517, G.519, A.520 Ligands: VL5.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.459

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