SMTL ID : 6zod.1

Fusidic acid binding to the allosteric deep transmembrane domain binding pocket, TM7/TM8 groove, and TM1/TM2 groove of the fully induced AcrB T protomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 9 residues within 4Å: Chain A: I.27, L.28, V.32, V.341, L.377, F.380, I.390 Ligands: LMT.12, FUA.13 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.27, A:I.27, A:V.32, A:V.341, A:L.377, A:F.380, A:I.390 LMT.3: 10 residues within 4Å: Chain A: R.8, F.11, I.18 Chain B: Q.439, G.440, M.447, C.887, A.890, L.891, K.955 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:M.447, B:A.890, A:I.18 Hydrogen bonds: B:Q.439, B:A.890, B:K.955, A:R.8 Salt bridges: A:R.8 LMT.11: 9 residues within 4Å: Chain A: G.440, V.443, G.444, M.447, C.887, A.890, L.891 Chain C: R.8, I.15 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.15, A:L.891, A:L.891 Hydrogen bonds: C:R.8, A:L.891 LMT.12: 9 residues within 4Å: Chain A: L.25, K.29 Chain B: A.451, V.454, F.458, N.871, Q.872, S.875 Ligands: LMT.1 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.454, B:F.458, B:F.458 Hydrogen bonds: B:Q.872, A:K.29 Salt bridges: A:K.29 LMT.31: 6 residues within 4Å: Chain C: L.28, L.30, V.32, L.344, F.380, I.390 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.344, C:F.380, C:I.390 Hydrogen bonds: C:L.28 LMT.34: 4 residues within 4Å: Chain C: A.22, A.385, F.386 Ligands: D12.37 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.22 LMT.35: 8 residues within 4Å: Chain C: S.530, G.533, I.534, R.536, S.537, Y.541, L.544, I.548 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.534, C:L.544, C:I.548, C:I.548 Hydrogen bonds: C:R.536, C:S.537, C:S.537, C:R.540, C:Y.541

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

EDO.2: 5 residues within 4Å: Chain A: Y.758, D.761, V.768, K.770 Chain B: Q.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.758 EDO.4: 5 residues within 4Å: Chain A: S.46, A.47, S.48, Q.125, G.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.125 EDO.6: 2 residues within 4Å: Chain A: G.959, L.960 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: K.510, G.511, W.515, R.518 No protein-ligand interaction detected (PLIP) EDO.9: 1 residues within 4Å: Chain A: K.589 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.589 EDO.10: 1 residues within 4Å: Chain A: G.533 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain B: N.231, S.233 Chain C: S.84 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.233, B:S.233, C:S.84 EDO.16: 4 residues within 4Å: Chain B: L.703, P.718, E.722 Chain D: R.26 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.722, D:R.26 EDO.18: 4 residues within 4Å: Chain B: K.248, R.259, L.261, R.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.248, B:R.259, B:R.263 EDO.19: 7 residues within 4Å: Chain A: E.309, K.312 Chain B: I.685, Q.687, Y.819, N.820, D.858 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.312, B:Q.687, B:N.820, B:D.858 EDO.29: 5 residues within 4Å: Chain A: Q.218, T.222 Chain B: G.51, D.276, G.755 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.222, A:T.222, B:D.276 EDO.30: 5 residues within 4Å: Chain B: Q.124, N.760, D.761 Chain C: Q.120, E.121 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.124, C:Q.120 EDO.33: 2 residues within 4Å: Chain B: R.168 Chain C: N.820 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.76, C:N.820 EDO.40: 3 residues within 4Å: Chain B: Y.811 Chain D: R.23, D.44 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.23, B:Y.811 EDO.41: 3 residues within 4Å: Chain B: N.700 Chain D: R.23, W.57 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.23

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: S.84, A.580, G.581, P.814 Chain C: N.231, A.232, S.233 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.233 GOL.15: 2 residues within 4Å: Chain B: Q.176, K.292 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.292, B:K.292

2 x D10: DECANE(Non-covalent)

D10.7: 7 residues within 4Å: Chain A: V.382, F.386, V.454, I.472, V.475, S.476, A.479 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.386 D10.20: 6 residues within 4Å: Chain B: M.1, F.4, F.5, F.11, I.15, I.487 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.4, B:F.5, B:I.487

4 x FUA: FUSIDIC ACID(Non-covalent)

FUA.13: 8 residues within 4Å: Chain A: G.24, I.27, L.28, K.334, I.337, H.338, V.341 Ligands: LMT.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.27, A:L.28, A:I.337, A:V.341 Salt bridges: A:H.338, A:H.338 FUA.26: 14 residues within 4Å: Chain B: V.452, Y.545, M.552, Y.877, S.880, L.881, V.884, L.888, M.902, L.903, P.906, L.932, I.935, A.939 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.877, B:L.881, B:L.881, B:V.884, B:L.888, B:L.903, B:P.906, B:I.935, B:A.939 Hydrogen bonds: B:Y.545, B:S.880 FUA.27: 7 residues within 4Å: Chain B: L.28, L.300, K.334, I.337, H.338, V.341 Ligands: 8K6.21 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.300, B:K.334, B:H.338, B:V.341 Salt bridges: B:H.338 FUA.28: 13 residues within 4Å: Chain B: E.339, T.343, E.346, A.347, L.350, V.399, L.400, G.930, T.933, T.934, F.982, G.985, V.986 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.347, B:L.350, B:V.399, B:V.986 Hydrogen bonds: B:T.343, B:E.346

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

PGE.17: 5 residues within 4Å: Chain B: F.617, T.678, R.717, L.828, G.829 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.717, B:R.717, B:G.829

1 x 8K6: Octadecane(Non-covalent)

8K6.21: 11 residues within 4Å: Chain B: I.27, N.298, L.300, D.301, I.337, V.341, L.344, L.376, F.380, I.390 Ligands: FUA.27 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.300, B:I.337, B:V.341, B:L.344, B:L.376, B:F.380, B:F.380, B:I.390

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

SO4.22: 4 residues within 4Å: Chain A: R.168 Chain B: M.76, Y.77, N.820 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.168 SO4.23: 4 residues within 4Å: Chain B: P.36, T.37, G.387, S.389 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.37 SO4.24: 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 SO4.25: 3 residues within 4Å: Chain B: K.55, G.691, H.692 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.692 Salt bridges: B:K.55 SO4.39: 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 PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.32: 13 residues within 4Å: Chain B: P.9, W.13, I.17, L.21, T.495 Chain C: I.882, F.885, E.893, S.894, W.895, S.896, K.950, R.1030 15 PLIP interactions: 8 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:I.882, C:W.895, C:W.895, C:W.895, B:P.9, B:W.13, B:W.13, B:I.17, B:I.17, B:L.21, B:T.495 Hydrogen bonds: C:W.895, C:S.896 Salt bridges: C:K.950, C:R.1030 PTY.36: 6 residues within 4Å: Chain B: L.25 Chain C: V.454, P.455, F.458, F.459, V.883 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.454, C:P.455, C:F.458, C:F.458, C:V.883

1 x D12: DODECANE(Non-covalent)

D12.37: 9 residues within 4Å: Chain C: F.386, F.388, V.454, A.457, R.468, S.471, I.472 Ligands: LMT.34, HEX.38 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.472

1 x HEX: HEXANE(Non-covalent)

HEX.38: 7 residues within 4Å: Chain C: V.382, F.386, V.475, S.476, A.479, L.480 Ligands: D12.37 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.386

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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