SMTL ID : 7ouk.1

BDM88855 inhibitor bound to the transmembrane domain of AcrB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 8 residues within 4Å: Chain A: I.27, L.28, V.32, H.338, V.341, L.376, F.380 Ligands: LMT.23 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.27, A:V.32, A:V.341, A:L.376, A:F.380, A:F.380 LMT.3: 9 residues within 4Å: Chain A: I.335, H.338, E.339, V.341, K.342, V.345, D.633, W.634, A.635 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.341, A:V.345 Hydrogen bonds: A:E.339 LMT.11: 9 residues within 4Å: Chain A: G.440, A.441, G.444, C.887, A.890, L.891 Chain C: R.8, F.11, I.18 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.11, C:I.18 Hydrogen bonds: C:R.8, A:G.440, A:E.893 LMT.16: 8 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, F.1020 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.17: 10 residues within 4Å: Chain B: I.27, N.298, L.300, D.301, A.304, K.334, I.337, V.341, L.377, F.380 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.27, B:I.337, B:V.341, B:L.377, B:F.380, B:F.380 Hydrogen bonds: B:N.298, B:D.301 LMT.23: 12 residues within 4Å: Chain A: L.25, L.28, K.29 Chain B: V.454, P.455, F.458, N.871, Q.872, S.875, L.876, V.883 Ligands: LMT.1 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.454, B:P.455, B:F.458, B:L.876, B:V.883 Hydrogen bonds: B:N.871, B:Q.872, B:S.875, B:S.875 Salt bridges: A:K.29 LMT.34: 9 residues within 4Å: Chain C: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, F.1020 Ligands: OCT.35 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.1020 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:R.540, C:Y.541 LMT.39: 6 residues within 4Å: Chain B: R.8 Chain C: G.440, L.891, Y.892, E.947, K.950 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.8, B:R.8, C:E.947, C:K.950, C:K.950

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

1K8.2: 14 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, L.944, E.947, F.948 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.411, A:I.438, A:A.441, A:I.445, A:L.944, A:E.947, A:F.948 Hydrogen bonds: A:L.404 Halogen bonds: A:K.940 1K8.29: 11 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 Ligands: SO4.31 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

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

EDO.4: 6 residues within 4Å: Chain A: P.50, R.185, E.273, G.755, Y.772, M.774 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.185, A:R.185 EDO.9: 5 residues within 4Å: Chain A: D.566, E.567, D.568, K.643, S.997 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.566, A:D.568 EDO.10: 4 residues within 4Å: Chain A: E.693, E.810 Chain E: Y.56, F.90 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:Y.56, A:E.693, A:E.810 Water bridges: A:E.693, A:R.808 EDO.12: 4 residues within 4Å: Chain A: D.99 Chain B: I.102 Chain C: D.99, I.102 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.99 EDO.13: 4 residues within 4Å: Chain A: Y.811 Chain E: E.20, R.23, D.44 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Y.811, E:D.44 EDO.14: 5 residues within 4Å: Chain A: N.231, S.233 Chain B: S.84, T.724, P.814 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.84, B:T.724, B:T.724 EDO.19: 5 residues within 4Å: Chain B: M.115, G.126, V.127 Chain C: Q.112, P.116 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.112, B:V.127 Water bridges: B:Q.112 EDO.20: 3 residues within 4Å: Chain B: N.74, T.98, D.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.99 Water bridges: B:N.74 EDO.26: 3 residues within 4Å: Chain B: S.537, G.539, R.540 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.539, B:R.540 EDO.27: 6 residues within 4Å: Chain B: Q.437, F.948, D.951, L.952, K.955, M.970 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.955, B:K.955 Water bridges: B:R.418 EDO.33: 4 residues within 4Å: Chain A: N.820, D.858 Chain C: E.309, K.312 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.858, C:K.312 Water bridges: A:N.820, A:N.820 EDO.41: 6 residues within 4Å: Chain A: S.84, G.581, T.724 Chain C: Q.218, N.231, S.233 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.581, A:T.724, A:T.724 Water bridges: C:S.233, C:S.233 EDO.42: 2 residues within 4Å: Chain C: S.46, G.126 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.125 EDO.43: 7 residues within 4Å: Chain C: G.675, T.676, A.677, D.681, N.719, E.826, L.828 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.677, C:E.826

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

OCT.5: 1 residues within 4Å: Chain A: W.895 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.895, A:W.895 OCT.32: 1 residues within 4Å: Chain C: W.13 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.13, C:W.13 OCT.35: 3 residues within 4Å: Chain C: S.523, S.530 Ligands: LMT.34 No protein-ligand interaction detected (PLIP)

3 x C14: TETRADECANE(Non-covalent)

C14.6: 4 residues within 4Å: Chain A: W.13, R.363, T.495, M.496 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.13 C14.8: 7 residues within 4Å: Chain A: F.386, A.457, F.458, R.468, I.472, V.475, S.476 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.457, A:F.458, A:V.475 C14.37: 4 residues within 4Å: Chain B: K.29 Chain C: F.458, F.459, V.883 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458, C:F.459, C:F.459, C:V.883

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: E.152, Y.182, E.269, L.270, G.271, G.272, Y.275 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.152, A:E.152, A:E.269, A:G.272 Water bridges: A:E.152 GOL.15: 7 residues within 4Å: Chain A: R.168, T.169, E.309 Chain B: L.75, M.76, Y.77, N.820 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.168, B:L.75 Water bridges: A:E.309, A:E.309 GOL.22: 5 residues within 4Å: Chain B: N.189, R.263, D.264, A.266, E.776 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.189, B:R.263 GOL.24: 9 residues within 4Å: Chain B: P.50, G.51, R.185, E.273, N.274, G.755, G.756, Y.772, M.774 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.185, B:R.185, B:G.755 Water bridges: B:Y.275 GOL.25: 4 residues within 4Å: Chain B: Q.210, E.245, K.248, I.249 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.245 GOL.40: 7 residues within 4Å: Chain C: R.185, E.273, N.274, G.755, G.756, Y.772, M.774 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.185, C:R.185, C:G.756 Water bridges: C:Y.275

1 x D10: DECANE(Non-covalent)

D10.18: 2 residues within 4Å: Chain B: W.13, T.495 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.13, B:T.495

1 x DDR: (2S)-3-hydroxypropane-1,2-diyl didecanoate(Non-covalent)

DDR.21: 9 residues within 4Å: Chain B: V.452, P.455, F.459, Y.467, F.556, L.876, Y.877, S.880, Q.928 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.455, B:F.459, B:Y.467, B:F.556, B:Y.877, B:Y.877 Hydrogen bonds: B:Q.928

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

DDQ.28: 8 residues within 4Å: Chain A: F.4, F.11, I.18 Chain B: G.440, G.444, M.447, C.887, A.890 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.11, A:I.18, B:A.890

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

SO4.30: 4 residues within 4Å: Chain B: N.361, F.362, R.363, K.498 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.362, B:R.363 SO4.31: 5 residues within 4Å: Chain B: Q.228, Q.229, L.230 Chain C: L.782 Ligands: 1K8.29 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.228, B:Q.229, B:L.230, B:L.230 SO4.44: 3 residues within 4Å: Chain C: K.55, G.691, H.692 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.692 Salt bridges: C:K.55

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

LPX.36: 6 residues within 4Å: Chain C: F.388, A.457, R.468, Q.469, S.471, I.472 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.457, C:I.472 Hydrogen bonds: C:Q.469, C:S.471 Salt bridges: C:R.468 LPX.38: 9 residues within 4Å: Chain B: I.10, L.21 Chain C: I.882, F.885, S.894, W.895, S.896, R.1030, 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:L.21 Hydrogen bonds: C:W.895, C:S.896, C:S.896 Salt bridges: C:R.1030

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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