SMTL ID : 7au1.1

Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 12)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 6 residues within 4Å: Chain A: E.249, N.348, P.350, Y.367, L.369, S.370 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.249 DMS.10: 5 residues within 4Å: Chain A: A.60, L.61, G.62, L.87, Q.91 No protein-ligand interaction detected (PLIP)

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

PEG.2: 6 residues within 4Å: Chain A: F.112, Y.113, P.114, G.116, N.227, N.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.227, A:N.229 PEG.3: 9 residues within 4Å: Chain A: H.121, E.134, G.135, N.241, I.245, F.341, P.342, G.343, E.344 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.121, A:G.135, A:N.241, A:P.342 PEG.9: 4 residues within 4Å: Chain A: T.176, L.177, A.178, R.396 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.176, A:A.178, A:R.396, A:R.396

1 x S08: 2-(6-(((R)-2-amino-2-oxo-1-phenylethyl)carbamoyl)-1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acetic acid(Covalent)

S08.4: 15 residues within 4Å: Chain A: S.252, K.255, R.289, D.290, V.291, R.293, S.307, N.309, Y.367, K.442, S.443, G.444, T.445, F.491, G.492 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.291, A:V.291 Hydrogen bonds: A:V.291, A:K.442, A:G.492 Water bridges: A:N.309, A:N.309, A:Y.367, A:T.445 Salt bridges: A:K.442

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: L.263, P.270, E.410, V.411, T.414 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.414 GOL.6: 4 residues within 4Å: Chain A: Q.405, V.406, S.408, P.409 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.405 GOL.7: 5 residues within 4Å: Chain A: M.48, T.49, A.50, K.51, E.52 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.48, A:K.51, A:E.52, A:E.52, A:E.52 GOL.8: 1 residues within 4Å: Chain A: Y.187 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain A: A.139, F.140, G.338, L.339, G.340 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.139 Water bridges: A:T.395

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newman, H. et al., High-Throughput Crystallography Reveals Boron-Containing Inhibitors of a Penicillin-Binding Protein with Di- and Tricovalent Binding Modes. J.Med.Chem. (2021)

Release Date

2021-08-11

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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