SMTL ID : 4dx5.1

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

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-3-2-mer

Ligands

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Y.758, D.761, K.769, K.770 Chain B: Q.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.758 Water bridges: A:Q.124, A:Q.181, A:K.770 GOL.10: 8 residues within 4Å: Chain A: P.50, R.185, E.273, N.274, G.755, G.756, Y.772, M.774 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.185, A:R.185 Water bridges: A:Y.772 GOL.12: 8 residues within 4Å: Chain A: A.165, R.168, E.309 Chain B: L.75, M.76, Y.77, M.78, N.820 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.168, A:R.168, A:E.309, B:M.78 Water bridges: A:E.309, A:K.312, B:L.75, B:M.76 GOL.13: 7 residues within 4Å: Chain B: L.111, Q.112, 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, B:V.127 GOL.24: 8 residues within 4Å: Chain B: F.727, I.729, P.783, I.786, S.802, S.805, S.806, S.807 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.805, B:S.807, B:S.807 GOL.26: 6 residues within 4Å: Chain B: N.231, A.232, S.233 Chain C: S.84, G.581, T.724 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:N.231, B:S.233, C:S.84, C:G.581 Water bridges: B:S.233, C:Q.622, C:N.623 GOL.27: 6 residues within 4Å: Chain B: R.239, N.760, D.761 Chain C: P.119, Q.120, E.121 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.761, C:Q.120, C:E.121 Water bridges: B:R.239, B:N.760, B:N.760 GOL.28: 7 residues within 4Å: Chain A: N.231, S.233 Chain B: S.84, A.580, G.581, T.724, P.814 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.581, B:T.724, B:T.724, A:S.233 Water bridges: A:Q.218, A:N.231, A:S.233 GOL.29: 5 residues within 4Å: Chain A: G.581, T.724 Chain C: Q.218, N.231, S.233 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.218, C:N.231, A:G.581, A:T.724 Water bridges: C:S.233 GOL.42: 7 residues within 4Å: Chain C: D.566, E.567, D.568, G.994, G.996, S.997, G.998 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.566, C:E.567, C:D.568, C:G.996 GOL.43: 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.755 GOL.45: 8 residues within 4Å: Chain C: Q.151, E.152, S.155, G.179, S.180, N.274, Y.275, I.277 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.155, C:S.180, C:S.180, C:N.274 Water bridges: C:S.155, C:D.156, C:A.286 GOL.49: 6 residues within 4Å: Chain B: T.696, N.700 Chain D: R.23, A.24, W.57, H.59 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.23, D:R.23, D:H.59, B:N.700 Water bridges: B:E.722 GOL.50: 7 residues within 4Å: Chain B: S.806 Chain D: I.114, N.122, D.143, F.145, K.147, I.152 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Water bridges: B:S.806, B:S.806, B:S.806 Hydrogen bonds: D:N.122, D:D.143, D:D.143 GOL.51: 3 residues within 4Å: Chain A: Y.811 Chain E: R.23, D.44 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.23, E:D.44, A:Y.811 Water bridges: E:E.20

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

LMT.2: 10 residues within 4Å: Chain A: I.27, L.28, V.32, V.341, L.344, I.348, P.373, L.376, F.380 Ligands: LMT.21 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.27, A:I.27, A:V.341, A:L.344, A:I.348, A:P.373, A:L.376, A:F.380 LMT.3: 13 residues within 4Å: Chain A: F.459, Y.467, F.556, S.561, G.870, N.871, Y.877, S.880, L.881, N.923, Q.928, L.931, I.935 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.877, A:Y.877, A:L.881, A:L.881, A:Q.928, A:L.931, A:I.935 Hydrogen bonds: A:Y.467, A:S.561, A:N.871, A:N.923, A:Q.928 LMT.4: 12 residues within 4Å: Chain A: G.440, G.444, M.447, C.887, A.890, L.891, D.951 Chain C: R.8, F.11, I.15, I.18, I.19 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:M.447, A:L.891, C:I.15, C:I.18, C:I.18, C:I.19 Hydrogen bonds: A:G.440, A:G.444, A:D.951, C:R.8 LMT.9: 9 residues within 4Å: Chain A: I.335, H.338, E.339, K.342, V.345, E.346, I.349, D.633, A.635 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.342, A:V.345, A:V.345, A:E.346, A:I.349 Hydrogen bonds: A:D.633, A:A.635 Salt bridges: A:K.342 LMT.15: 10 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, V.1016, I.1019, F.1020 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.1016, B:I.1019, B:F.1020 Hydrogen bonds: B:R.536, B:R.536, B:S.537, B:R.540, B:R.540, B:R.540, B:Y.541 LMT.21: 11 residues within 4Å: Chain A: L.28, K.29 Chain B: S.450, A.451, V.454, F.458, N.871, Q.872, L.876, I.879 Ligands: LMT.2 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.454, B:F.458, B:F.458, B:L.876, B:I.879 Hydrogen bonds: B:N.871, B:N.871, B:Q.872, A:K.29 Salt bridges: A:K.29 LMT.22: 10 residues within 4Å: Chain B: Y.467, F.556, E.866, Y.877, S.880, L.881, V.884, N.923, Q.928, L.932 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.877, B:Y.877, B:L.881, B:V.884, B:Q.928, B:Q.928, B:L.932 Hydrogen bonds: B:Y.467, B:E.866, B:N.923, B:Q.928 LMT.30: 10 residues within 4Å: Chain C: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, I.1019, F.1020 Ligands: D10.48 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.534, C:I.1019, C:F.1020, C:F.1020 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:R.540, C:Y.541

7 x OCT: N-OCTANE(Non-covalent)(Non-functional Binders)

OCT.5: 6 residues within 4Å: Chain A: F.885, W.895, S.896, F.899, F.1033 Ligands: OCT.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.895, A:F.899 OCT.6: 6 residues within 4Å: Chain A: F.885, L.886, W.895 Chain C: I.17 Ligands: OCT.5, D12.32 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.895, A:W.895 OCT.31: 7 residues within 4Å: Chain B: I.17, L.21 Chain C: I.882, F.885, L.886, W.895 Ligands: C14.20 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.895, C:W.895 OCT.33: 8 residues within 4Å: Chain B: I.10 Chain C: E.893, S.894, W.895, S.896, I.897, K.950, F.1033 No protein-ligand interaction detected (PLIP) OCT.34: 3 residues within 4Å: Chain C: G.440, V.443, L.891 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.891 OCT.40: 8 residues within 4Å: Chain C: A.446, M.447, S.450, V.454, V.475, A.479, V.482 Ligands: HEX.38 No protein-ligand interaction detected (PLIP) OCT.44: 7 residues within 4Å: Chain C: M.552, A.553, F.556, Y.877, V.909, L.931, I.935 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.909

6 x D10: DECANE(Non-covalent)

D10.7: 4 residues within 4Å: Chain A: W.13, I.17 Chain B: W.895 Ligands: D10.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.13, A:W.13 D10.16: 7 residues within 4Å: Chain A: I.17 Chain B: I.882, F.885, L.886, W.895 Ligands: D10.7, D12.17 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.886, B:W.895, B:W.895, A:I.17 D10.18: 7 residues within 4Å: Chain B: I.27, N.298, L.300, D.301, I.337, F.380, I.390 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.300 D10.35: 3 residues within 4Å: Chain C: M.1, F.4, F.5 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.4 D10.37: 6 residues within 4Å: Chain B: I.18, A.22, L.25, K.29 Chain C: F.458 Ligands: D12.36 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.458, C:F.458, B:L.25 D10.48: 6 residues within 4Å: Chain C: S.523, H.526, Y.527, S.530, F.1020 Ligands: LMT.30 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.527

5 x HEX: HEXANE(Non-covalent)

HEX.8: 10 residues within 4Å: Chain A: D.566, E.567, D.568, W.634, K.643, G.994, A.995, G.996, S.997, G.998 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.568 HEX.19: 3 residues within 4Å: Chain B: M.1, F.4, F.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.4, B:F.4, B:F.5 HEX.23: 5 residues within 4Å: Chain B: M.1, V.443, A.446, L.483, L.486 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.483 HEX.38: 6 residues within 4Å: Chain C: V.382, V.475, S.476, A.479, L.480 Ligands: OCT.40 No protein-ligand interaction detected (PLIP) HEX.41: 7 residues within 4Å: Chain C: I.27, V.32, I.337, V.341, F.380, I.390, M.395 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.380

4 x D12: DODECANE(Non-covalent)

D12.11: 11 residues within 4Å: Chain A: F.4, R.8, F.11, V.14 Chain B: G.440, V.443, G.444, M.447, C.887, A.890, L.891 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.443, B:M.447, B:A.890, B:L.891, A:F.11 D12.17: 6 residues within 4Å: Chain B: F.885, W.895, S.896, F.899, F.1033 Ligands: D10.16 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.885, B:F.899, B:F.899, B:F.1033 D12.32: 6 residues within 4Å: Chain A: W.895 Chain C: W.13, I.17, M.20, M.496 Ligands: OCT.6 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.13 D12.36: 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: D10.37 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458, C:F.458

1 x MIY: (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE(Non-covalent)

MIY.14: 14 residues within 4Å: Chain B: S.48, Q.151, L.177, F.178, G.179, S.180, E.273, N.274, D.276, I.277, A.279, V.612, F.615, R.620 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.178, B:A.279 Hydrogen bonds: B:S.48, B:Q.151, B:G.179, B:D.276, B:D.276, B:R.620, B:R.620 Water bridges: B:S.155, B:S.155, B:S.180, B:E.273

1 x C14: TETRADECANE(Non-covalent)

C14.20: 8 residues within 4Å: Chain B: P.9, I.10, W.13, I.17, M.20, T.495 Chain C: W.895 Ligands: OCT.31 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.895, B:I.17, B:I.17

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

LMU.25: 11 residues within 4Å: Chain B: Y.327, 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:Y.327, B:F.617, B:F.628, B:V.672 Hydrogen bonds: B:D.566 Water bridges: B:N.667, B:A.670

1 x DD9: nonane(Non-covalent)

DD9.39: 5 residues within 4Å: Chain C: F.388, A.457, R.468, S.471, I.472 No protein-ligand interaction detected (PLIP)

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

SO4.46: 3 residues within 4Å: Chain C: K.55, G.691, H.692 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.692 Water bridges: C:K.55, C:K.55 Salt bridges: C:K.55

1 x UND: UNDECANE(Non-covalent)

UND.47: 6 residues within 4Å: Chain C: L.353, V.354, Y.356, L.357, F.512, F.513 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.353, C:F.512, C:F.513

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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