SMTL ID : 6zo5.1

Fusidic acid binding to the TM1/TM2 groove of AcrB-G619P_G621P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-2-mer

Ligands

1 x XPE: 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL(Non-covalent)

XPE.1: 3 residues within 4Å: Chain A: G.957, G.959, L.960 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.1031

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

LMT.2: 9 residues within 4Å: Chain A: I.27, L.28, L.30, V.32, V.341, L.344, P.373, F.380, I.390 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.27, A:V.341, A:V.341, A:L.344, A:P.373, A:F.380, A:I.390 LMT.3: 9 residues within 4Å: Chain A: G.440, G.444, M.447, C.887, A.890, L.891 Chain C: R.8, F.11, I.18 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:A.890 Hydrogen bonds: A:G.440, A:G.444, C:R.8 LMT.4: 15 residues within 4Å: Chain A: L.25, L.28, K.29 Chain B: M.447, S.450, A.451, V.454, P.455, F.458, N.871, Q.872, S.875, L.876, I.879, V.883 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.454, B:P.455, B:F.458, B:F.458, B:I.879, B:V.883 Hydrogen bonds: B:F.458, B:Q.872, B:S.875, A:L.25, A:K.29 Salt bridges: A:K.29, A:K.29 LMT.5: 9 residues within 4Å: Chain A: S.530, G.533, I.534, R.536, Y.541, L.544, I.548, L.1017, F.1020 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.534, A:L.544, A:L.544, A:I.548, A:L.1017, A:F.1020 Hydrogen bonds: A:R.536, A:Y.541 LMT.18: 10 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.1017, F.1020 Ligands: D12.21 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.534, B:Y.541, B:L.1017, B:F.1020 Hydrogen bonds: B:R.536, B:S.537, B:S.537, B:R.540, B:Y.541 LMT.19: 11 residues within 4Å: Chain B: I.27, V.32, N.298, L.300, D.301, K.334, I.337, V.341, I.348, F.380 Ligands: FUA.17 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.27, B:I.337, B:V.341, B:I.348 Hydrogen bonds: B:N.298, B:D.301, B:D.301, B:D.301, B:K.334 Water bridges: B:I.27, B:A.304 LMT.20: 11 residues within 4Å: Chain A: R.8, F.11, I.15, I.18 Chain B: G.440, V.443, G.444, M.447, C.887, A.890, L.891 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.11, A:F.11, A:I.15, A:I.18, B:V.443, B:A.890 Hydrogen bonds: A:R.8, B:A.890 LMT.39: 9 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541, L.544, I.548, F.1020 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.544, C:I.548, C:F.1020, C:F.1020, C:F.1020 Hydrogen bonds: C:S.530, C:R.536, C:R.536, C:S.537, C:R.540, C:R.540, C:Y.541

4 x D12: DODECANE(Non-covalent)

D12.6: 2 residues within 4Å: Chain A: W.13 Chain B: W.895 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.13, A:W.13 D12.7: 4 residues within 4Å: Chain A: A.457, F.458, R.468, I.472 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.458, A:I.472 D12.21: 3 residues within 4Å: Chain B: S.523, L.976 Ligands: LMT.18 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.976 D12.40: 2 residues within 4Å: Chain C: F.4, F.5 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.4, C:F.5

5 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.8: 1 residues within 4Å: Chain A: W.895 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.895, A:W.895 D10.9: 1 residues within 4Å: Chain A: K.29 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.29 D10.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.24: 2 residues within 4Å: Chain B: G.511, W.515 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.515, B:W.515, B:W.515 D10.43: 5 residues within 4Å: Chain C: S.96, A.457, F.458, R.468 Ligands: LPX.34 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.458

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: R.259, L.261, R.263, D.264 Chain D: I.154, N.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.259, A:R.263, A:D.264 Water bridges: A:R.263 GOL.11: 8 residues within 4Å: Chain A: P.50, R.185, E.273, N.274, G.755, Y.772, M.774 Ligands: EDO.52 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.185, A:R.185, A:E.273, C:T.222 Water bridges: A:Y.275 GOL.12: 6 residues within 4Å: Chain A: T.696, R.699, N.700 Chain E: R.23, W.57, H.59 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:R.699, A:N.700, A:N.700, E:R.23, E:H.59 GOL.27: 9 residues within 4Å: Chain A: A.165, R.168, T.169, E.309 Chain B: L.75, M.76, Y.77, M.78, N.820 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:M.78, A:R.168, A:E.309 Water bridges: B:N.820, A:E.309 GOL.45: 8 residues within 4Å: Chain C: F.617, G.675, T.676, A.677, D.681, N.719, E.826, L.828 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.676, C:A.677, C:A.677, C:N.719, C:E.826 Water bridges: C:S.134 GOL.46: 7 residues within 4Å: Chain A: V.64, Q.67, L.117 Chain C: E.273, Y.758, D.761, K.770 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.273, C:Y.758, C:Y.758 Water bridges: C:Q.181, C:E.273 GOL.47: 8 residues within 4Å: Chain C: R.185, E.273, N.274, G.755, G.756, Y.772, M.774 Ligands: PGE.37 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.185, C:R.185, C:E.273, C:G.756 Water bridges: C:Y.275 GOL.48: 6 residues within 4Å: Chain C: E.417, R.418, A.421, H.505, E.521, R.973 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.417 Water bridges: C:E.414, C:E.414, C:E.521

7 x HEX: HEXANE(Non-covalent)

HEX.13: 5 residues within 4Å: Chain A: F.556, N.871, A.873, N.923, Q.928 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.556, A:A.873, A:Q.928 HEX.14: 2 residues within 4Å: Chain A: H.338, K.342 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.338, A:K.342 HEX.28: 1 residues within 4Å: Chain B: F.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.4 HEX.29: 2 residues within 4Å: Chain B: F.885, F.899 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.885, B:F.885, B:F.899 HEX.30: 4 residues within 4Å: Chain B: M.20, L.21, G.24 Ligands: FUA.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.21 HEX.49: 3 residues within 4Å: Chain C: S.523, Y.527, F.1020 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.527, C:F.1020 HEX.50: 2 residues within 4Å: Chain C: F.380, I.390 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.380, C:I.390

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

EDO.15: 4 residues within 4Å: Chain A: T.243, G.247, R.263, I.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.243 Water bridges: A:I.268 EDO.31: 4 residues within 4Å: Chain B: K.163, S.180, Q.181, E.273 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.181, B:Q.181, B:E.273 EDO.32: 6 residues within 4Å: Chain B: Y.325, P.326, Y.327, D.328, Q.569, V.571 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.325, B:D.328, B:Q.569 EDO.33: 3 residues within 4Å: Chain B: D.745, R.792, A.793 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.792, B:R.792 EDO.52: 7 residues within 4Å: Chain A: G.51, G.755, M.774 Chain C: Q.218, G.221, T.222 Ligands: GOL.11 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.222, A:G.51, A:G.755 Water bridges: C:Q.218, C:Q.218, C:G.221 EDO.53: 4 residues within 4Å: Chain C: K.208, N.211, R.239, N.760 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.208, C:R.239, C:R.239, C:N.760 Water bridges: C:D.761 EDO.54: 2 residues within 4Å: Chain D: A.75, Y.76 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.76

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

DDR.16: 14 residues within 4Å: Chain B: V.452, P.455, F.459, M.552, F.556, L.876, Y.877, S.880, L.881, V.884, V.905, Q.928, L.932, I.935 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.556, B:L.881, B:V.884, B:V.905, B:Q.928, B:I.935 Hydrogen bonds: B:Y.877

1 x FUA: FUSIDIC ACID(Non-covalent)

FUA.17: 9 residues within 4Å: Chain B: G.24, I.27, L.300, K.334, I.337, H.338, V.341 Ligands: LMT.19, HEX.30 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.27, B:I.27, B:L.300, B:I.337, B:V.341 Salt bridges: B:H.338, B:H.338

3 x C14: TETRADECANE(Non-covalent)

C14.22: 3 residues within 4Å: Chain B: W.13 Chain C: W.895 Ligands: LPX.36 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.13, B:W.13 C14.41: 1 residues within 4Å: Chain C: F.458 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458 C14.42: 1 residues within 4Å: Chain C: W.13 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.13

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

SO4.25: 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 SO4.26: 4 residues within 4Å: Chain B: K.55, G.691, H.692, E.693 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.692 Water bridges: B:K.55, B:K.55, B:E.693 Salt bridges: B:K.55 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.34: 10 residues within 4Å: Chain C: V.382, F.386, G.387, F.388, A.457, R.468, S.471, I.472, S.476 Ligands: D10.43 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.382, C:I.472 Hydrogen bonds: C:G.387 Water bridges: C:Q.469 Salt bridges: C:R.468 LPX.36: 10 residues within 4Å: Chain B: I.17, L.21 Chain C: F.885, S.894, W.895, S.896, K.950, R.1030, F.1033 Ligands: C14.22 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.885, C:W.895, B:I.17, B:L.21 Hydrogen bonds: C:W.895, C:S.896, C:K.950, C:R.1030

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.35: 3 residues within 4Å: Chain C: G.957, G.959, L.960 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.957, C:L.960 PGE.37: 5 residues within 4Å: Chain C: G.756, S.757, Y.758, Y.772 Ligands: GOL.47 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.758, C:Y.772

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.38: 11 residues within 4Å: Chain B: R.8, F.11, I.18 Chain C: Q.439, V.443, M.447, A.890, L.891, Y.892, I.897, K.950 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:V.443, C:A.890, C:L.891, B:F.11, B:F.11, B:I.18 Hydrogen bonds: C:K.950 Salt bridges: B:R.8

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

OCT.51: 4 residues within 4Å: Chain C: M.552, F.556, Y.877, V.909 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.556, C:F.556, C:Y.877, C:V.909

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tam, H.K. et al., Allosteric drug transport mechanism of multidrug transporter AcrB. Nat Commun (2021)

Release Date

2021-05-19

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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