SMTL ID : 7oum.1

BDM88855 inhibitor bound to the transmembrane domain of AcrB-R971A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-3-2-mer

Ligands

7 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 10 residues within 4Å: Chain A: G.440, A.441, G.444, C.887, A.890, L.891 Chain C: F.4, R.8, F.11, I.18 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.11, C:I.18, C:I.18, A:A.890 Hydrogen bonds: C:R.8, C:R.8, A:G.440, A:G.444 Salt bridges: C:R.8 LMT.2: 6 residues within 4Å: Chain A: I.27, L.28, V.32, V.341, I.348 Ligands: LMT.19 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.27, A:V.341, A:V.341, A:I.348 Water bridges: A:L.28 LMT.7: 7 residues within 4Å: Chain A: I.335, H.338, E.339, V.341, V.345, D.633, A.635 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.341, A:V.345 Hydrogen bonds: A:E.339, A:D.633, A:A.635 LMT.13: 9 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, F.1020 Ligands: D10.23 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.534, B:F.1020 Hydrogen bonds: B:R.536, B:S.537, B:S.537, B:R.540, B:Y.541 LMT.14: 13 residues within 4Å: Chain B: I.27, V.32, N.298, L.300, D.301, K.334, I.337, V.341, L.344, I.348, L.377, F.380, I.390 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.27, B:I.337, B:V.341, B:L.344, B:I.348, B:L.377 Hydrogen bonds: B:N.298, B:D.301, B:K.334, B:K.334 LMT.19: 10 residues within 4Å: Chain A: L.25, K.29 Chain B: S.450, V.454, F.458, N.871, Q.872, S.875, L.876 Ligands: LMT.2 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.458, B:F.458, B:L.876, A:L.25 Hydrogen bonds: B:N.871, B:Q.872, B:S.875, A:K.29 Salt bridges: A:K.29 LMT.27: 11 residues within 4Å: Chain C: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.544, F.1020, F.1021 Ligands: OCT.35 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.544, C:F.1020, C:F.1021 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:R.540, C:Y.541

1 x C14: TETRADECANE(Non-covalent)

C14.3: 5 residues within 4Å: Chain A: A.457, F.458, R.468, I.472, S.476 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.458, A:F.458, A:F.458, A:I.472

2 x DDQ: DECYLAMINE-N,N-DIMETHYL-N-OXIDE(Non-covalent)

DDQ.4: 2 residues within 4Å: Chain A: W.13, I.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.13, A:I.17 DDQ.28: 3 residues within 4Å: Chain C: W.13, L.492, T.495 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.495

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: P.50, G.51, R.185, E.273, N.274, G.755, Y.772, M.774 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.51, A:R.185, A:R.185, A:E.273 Water bridges: A:Y.275 GOL.17: 8 residues within 4Å: Chain B: F.727, P.783, I.786, S.802, S.805, S.806, S.807 Chain D: K.144 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:P.783, B:S.805, B:S.807, D:K.144 Water bridges: B:S.807 GOL.37: 7 residues within 4Å: Chain C: R.185, E.273, N.274, G.755, G.756, Y.772, M.774 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.185, C:R.185, C:G.756

2 x 1K8: 3-chloranyl-2-piperazin-1-yl-quinoline(Non-covalent)

1K8.6: 12 residues within 4Å: Chain A: L.404, D.407, D.408, V.411, I.438, A.441, L.442, I.445, A.446, L.449, K.940, E.947 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.411, A:I.438, A:A.441, A:I.445, A:E.947 Hydrogen bonds: A:L.404 Halogen bonds: A:K.940 1K8.25: 10 residues within 4Å: Chain B: L.219, Q.228, L.230, N.231, A.232 Chain C: P.725, M.781, P.783, W.809, Y.811 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.219, B:L.230, B:A.232, C:W.809 pi-Stacking: C:W.809

4 x D10: DECANE(Non-covalent)

D10.8: 4 residues within 4Å: Chain A: F.458, L.876 Chain C: L.25, K.29 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:L.25, C:K.29, A:F.458, A:F.458, A:L.876 D10.11: 1 residues within 4Å: Chain A: W.895 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.895, A:W.895 D10.23: 3 residues within 4Å: Chain B: Y.527, S.530 Ligands: LMT.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.527 D10.29: 2 residues within 4Å: Chain B: K.29 Chain C: F.458 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.458

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 3 residues within 4Å: Chain A: D.745, R.792, A.793 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: Q.124, Y.758, V.759, N.760 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: R.168, E.309 Chain B: L.75, M.76, Y.77, M.78, N.820 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: G.766 Chain B: K.55, G.691, H.692 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: N.231, S.233 Chain B: T.724, P.814 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: R.185, E.273, N.274, G.755, Y.772, M.774 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: R.239, N.760, D.761 Chain C: P.119, Q.120, E.121 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: K.208, A.209 Chain B: I.743, N.744, N.747 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: S.537, T.538, G.539, R.540 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: N.189, R.263, D.264, A.266, K.267 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain A: G.581, T.724 Chain C: Q.218, N.231, A.232, S.233 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain C: D.761, K.770 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain C: M.662, R.699, P.718, E.722 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain C: S.46, Q.89 Ligands: EDO.40 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain C: S.46, A.47, S.48, G.126 Ligands: EDO.39 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain D: D.143, F.145, K.147 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain A: Y.811 Chain E: E.20, R.23, D.44 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.26: 4 residues within 4Å: Chain B: N.361, F.362, R.363, K.498 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.362, B:R.363 Salt bridges: B:K.498 SO4.41: 3 residues within 4Å: Chain C: K.55, G.691, H.692 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.692 Water bridges: C:E.693 Salt bridges: C:K.55

4 x OCT: N-OCTANE(Non-covalent)

OCT.30: 1 residues within 4Å: Chain C: F.380 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.380 OCT.34: 4 residues within 4Å: Chain C: A.553, F.556, V.909, I.935 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.556, C:F.556, C:V.909, C:I.935 OCT.35: 3 residues within 4Å: Chain C: S.523, Y.527 Ligands: LMT.27 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.527 OCT.38: 1 residues within 4Å: Chain C: S.476 No protein-ligand interaction detected (PLIP)

1 x LPX: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate(Non-covalent)

LPX.32: 8 residues within 4Å: Chain B: I.17 Chain C: I.882, F.885, E.893, S.894, W.895, S.896, F.1033 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.882, C:F.885, C:W.895, C:W.895, B:I.17 Hydrogen bonds: C:W.895, C:S.896, C:S.896, C:S.896

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ple, C. et al., Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps. Nat Commun (2022)

Release Date

2021-12-29

Peptides

Multidrug efflux pump subunit AcrB: ABC
DARPIN: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Multidrug efflux pump subunit AcrB

DARPIN

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