SMTL ID : 8p1i.1

Single particle cryo-EM co-structure of Klebsiella pneumoniae AcrB with the BDM91288 efflux pump inhibitor at 2.97 Angstrom resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

1 x WQW: 3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline(Non-covalent)

WQW.1: 20 residues within 4Å: Chain A: L.404, L.405, D.407, D.408, V.411, N.415, R.418, I.438, A.441, L.442, I.445, A.446, L.449, V.482, K.939, I.942, L.943, E.946, F.947, D.950 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.411, A:V.411, A:I.438, A:A.441, A:I.445, A:L.943 Hydrogen bonds: A:D.408, A:D.950, A:D.950 Halogen bonds: A:K.939

1 x WR6: [(2~{R})-1-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-3-undecanoyloxy-propan-2-yl] tricosanoate(Non-covalent)

WR6.2: 27 residues within 4Å: Chain A: I.18, L.25, K.29 Chain B: V.382, F.386, M.447, S.450, A.451, I.454, P.455, A.457, F.458, F.459, G.460, R.468, I.472, V.475, S.476, A.479, L.480, N.870, Q.871, A.874, L.875, I.878, V.882, C.886 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.454, B:F.458, B:F.458, B:V.475, B:A.479, B:I.878 Hydrogen bonds: B:N.870, B:Q.871 Salt bridges: A:K.29, A:K.29

2 x PG8: 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)(Non-covalent)

PG8.3: 17 residues within 4Å: Chain C: V.382, F.386, F.388, A.446, M.447, S.450, I.454, A.457, R.468, S.471, I.472, V.475, S.476, A.479, L.480, V.482, L.483 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.454, C:A.479 Hydrogen bonds: C:I.472 PG8.4: 8 residues within 4Å: Chain A: F.458 Chain C: A.22, S.26, A.381, A.384, A.385, F.386, G.387 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.458, C:A.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vieira Da Cruz, A. et al., Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae. Embo Mol Med (2024)

Release Date

2024-01-17

Peptides

Efflux pump membrane transporter: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Efflux pump membrane transporter