SMTL ID : 4dx7.1

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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: I.27, L.28, V.32, I.337, V.341, P.373, L.377, F.380, I.390 Ligands: LMT.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.27, A:I.337, A:V.341, A:P.373, A:L.377, A:F.380, A:F.380, A:I.390 Water bridges: A:D.301 LMT.2: 10 residues within 4Å: Chain A: F.556, S.561, N.871, Y.877, S.880, L.881, V.884, N.923, Q.928, I.935 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.877, A:L.881, A:V.884, A:I.935 Hydrogen bonds: A:S.561, A:N.871, A:N.923, A:Q.928 Water bridges: A:T.463, A:Y.467 LMT.3: 10 residues within 4Å: Chain A: G.440, G.444, M.447, C.887, A.890, L.891 Chain C: R.8, F.11, I.15, I.18 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.11, C:I.15, C:I.18, C:I.18, A:L.891 Hydrogen bonds: C:R.8, A:G.440, A:A.890 Salt bridges: C:R.8 LMT.4: 7 residues within 4Å: Chain A: I.335, H.338, E.339, K.342, I.349, D.633, A.635 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.338, A:K.342, A:I.349 Hydrogen bonds: A:D.633, A:A.635 Water bridges: A:E.339 Salt bridges: A:K.342 LMT.10: 9 residues within 4Å: Chain A: L.28 Chain B: V.454, F.458, N.871, Q.872, S.875, L.876, V.883 Ligands: LMT.1 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Salt bridges: A:K.29 Hydrophobic interactions: B:V.454, B:F.458, B:F.458, B:F.458, B:V.883 Hydrogen bonds: B:N.871, B:Q.872, B:S.875 LMT.11: 8 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.976 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.976 Hydrogen bonds: B:R.536, B:S.537, B:S.537, B:R.540, B:R.540, B:Y.541 LMT.19: 8 residues within 4Å: Chain C: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, F.1020 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:R.540, C:Y.541

3 x DM2: DOXORUBICIN(Non-covalent)

DM2.5: 14 residues within 4Å: Chain A: M.575, G.616, F.617, A.618, T.676, G.679, D.681, R.717, N.719, R.815, E.826, Q.830, M.862 Ligands: DM2.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.617 Hydrogen bonds: A:F.617, A:D.681, A:N.719, A:R.815, A:E.826 Water bridges: A:T.624 DM2.6: 12 residues within 4Å: Chain A: S.134, M.575, F.617, F.664, F.666, N.667, L.668, T.676, A.677, R.717, Q.830 Ligands: DM2.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.617, A:F.664, A:T.676 Hydrogen bonds: A:N.667, A:N.667, A:T.676 pi-Stacking: A:F.617, A:F.617, A:F.666, A:F.666 DM2.13: 9 residues within 4Å: Chain B: S.46, Q.89, E.130, Q.176, F.178, G.179, I.277, V.612, F.615 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.178, B:F.178, B:V.612, B:F.615 Hydrogen bonds: B:Q.89, B:Q.89, B:Q.176 pi-Stacking: B:F.178

4 x D12: DODECANE(Non-covalent)

D12.7: 9 residues within 4Å: Chain A: R.8, F.11 Chain B: G.440, V.443, G.444, M.447, C.887, A.890, L.891 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.891, A:F.11 D12.18: 9 residues within 4Å: Chain B: L.25, K.29 Chain C: V.454, P.455, F.458, F.459, I.879, V.883 Ligands: D10.22 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458, C:F.458, C:F.459, C:V.883 D12.20: 6 residues within 4Å: Chain B: I.17 Chain C: F.885, L.886, W.895, F.1033 Ligands: D10.14 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.895, C:W.895 D12.24: 5 residues within 4Å: Chain A: W.895 Chain C: W.13, I.17, M.20 Ligands: D10.8 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.13, C:W.13

4 x D10: DECANE(Non-covalent)

D10.8: 6 residues within 4Å: Chain A: F.885, L.886, W.895 Chain C: I.17 Ligands: D10.9, D12.24 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.895, A:W.895, A:W.895 D10.9: 6 residues within 4Å: Chain A: F.885, W.895, S.896, F.899, F.1033 Ligands: D10.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.885 D10.14: 5 residues within 4Å: Chain B: W.13, I.17, M.20 Chain C: W.895 Ligands: D12.20 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.13, B:W.13, B:I.17, C:W.895 D10.22: 5 residues within 4Å: Chain B: A.22, L.25, K.29 Chain C: F.458 Ligands: D12.18 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.25, C:F.458, C:F.458

1 x LMU: DODECYL-ALPHA-D-MALTOSIDE(Non-covalent)

LMU.12: 10 residues within 4Å: Chain B: D.566, M.573, F.617, F.628, F.664, F.666, N.667, L.668, P.669, V.672 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.617, B:F.617, B:F.628, B:V.672 Hydrogen bonds: B:L.668 Water bridges: B:N.667, B:A.670

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 7 residues within 4Å: Chain B: Q.124, R.239, Y.758, N.760, D.761 Chain C: P.119, Q.120 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.124, B:R.239, B:D.761, B:D.761, B:D.761, C:Q.120 Water bridges: B:N.760 GOL.16: 10 residues within 4Å: Chain B: F.727, I.729, P.783, I.786, S.802, S.805, S.806, S.807 Chain D: N.112, K.144 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.805 Water bridges: B:P.783, B:D.784 GOL.21: 8 residues within 4Å: Chain C: R.185, E.273, N.274, G.755, G.756, S.757, Y.772, M.774 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.185, C:R.185, C:G.756 Water bridges: C:N.274, C:Y.758

2 x HEX: HEXANE(Non-covalent)

HEX.17: 5 residues within 4Å: Chain B: I.27, V.32, N.298, I.337, I.390 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.337, B:I.390 HEX.23: 7 residues within 4Å: Chain C: V.382, I.472, V.475, S.476, A.479, L.480, L.483 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.475

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eicher, T. et al., Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-05-02

Peptides

Acriflavine resistance protein B: 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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Acriflavine resistance protein B

DARPIN

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