SMTL ID : 6q4o.1

Fusidic acid bound AcrB_I27A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 11 residues within 4Å: Chain A: A.27, L.28, K.29, L.30, V.32, D.301, V.341, P.373, L.377, F.380, I.390 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.341, A:P.373, A:L.377, A:F.380 Hydrogen bonds: A:L.30, A:L.30 LMT.2: 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: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.440, C:R.8 Hydrophobic interactions: C:F.11, C:I.18 LMT.3: 10 residues within 4Å: Chain A: R.8, F.11 Chain B: Q.439, G.440, V.443, G.444, M.447, C.887, A.890, L.891 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.11, B:V.443, B:A.890 Hydrogen bonds: A:R.8, B:Q.439, B:A.890 Salt bridges: A:R.8 LMT.4: 8 residues within 4Å: Chain A: S.530, G.533, I.534, R.536, S.537, Y.541, F.1020 Ligands: OCT.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.1020 Hydrogen bonds: A:R.536, A:R.536, A:S.537, A:S.537, A:Y.541 LMT.16: 12 residues within 4Å: Chain B: A.27, L.28, V.32, N.298, L.300, D.301, K.334, V.341, V.345, F.380, I.390 Ligands: FUA.15 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.341, B:V.345, B:F.380, B:F.380, B:I.390 Hydrogen bonds: B:N.298, B:D.301, B:D.301, B:D.301 LMT.17: 11 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.544, I.547, F.1020 Ligands: D10.20 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.544, B:I.547 Hydrogen bonds: B:R.536, B:S.537, B:S.537, B:Y.541 LMT.36: 8 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541, F.1020 Ligands: D12.56 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.37: 6 residues within 4Å: Chain C: R.558, G.834, G.911, T.917, F.918, R.919 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.918, C:R.919 Hydrogen bonds: C:R.558, C:R.558, C:G.834

8 x D10: DECANE(Non-covalent)

D10.5: 4 residues within 4Å: Chain A: A.22, K.29 Ligands: OCT.14, D10.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.22 D10.6: 3 residues within 4Å: Chain A: W.13 Chain B: W.895 Ligands: D10.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.13, A:W.13, A:W.13 D10.18: 3 residues within 4Å: Chain B: W.895 Ligands: D10.6, D12.34 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.895, B:W.895, B:W.895 D10.19: 5 residues within 4Å: Chain A: K.29 Chain B: A.451, F.458, L.876 Ligands: D10.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.458, B:F.458, B:L.876 D10.20: 4 residues within 4Å: Chain B: S.523, Y.527, S.530 Ligands: LMT.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.527 D10.38: 3 residues within 4Å: Chain C: A.457, F.458 Ligands: DDQ.41 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458 D10.39: 5 residues within 4Å: Chain C: M.552, F.556, V.557, V.909, I.935 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.556, C:F.556, C:V.557, C:V.909, C:I.935 D10.40: 2 residues within 4Å: Chain C: F.512, W.515 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.515

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

DDQ.7: 2 residues within 4Å: Chain A: W.515, R.518 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.515 DDQ.8: 2 residues within 4Å: Chain A: F.388, Q.469 No protein-ligand interaction detected (PLIP) DDQ.9: 3 residues within 4Å: Chain A: F.458 Chain C: L.25, K.29 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.25, A:F.458 DDQ.21: 7 residues within 4Å: Chain B: F.386, A.457, F.458, R.468, I.472, V.475, S.476 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.472, B:V.475 Hydrogen bonds: B:R.468 Water bridges: B:R.468 pi-Cation interactions: B:F.458 DDQ.22: 3 residues within 4Å: Chain B: G.511, W.515, R.518 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.515 DDQ.23: 4 residues within 4Å: Chain B: A.381, A.384 Ligands: OCT.33, PTY.51 No protein-ligand interaction detected (PLIP) DDQ.24: 4 residues within 4Å: Chain B: F.556, Y.877, L.881 Ligands: DDR.35 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.556, B:Y.877, B:L.881 DDQ.41: 5 residues within 4Å: Chain C: F.388, R.468, S.471, I.472 Ligands: D10.38 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.388, C:I.472 DDQ.42: 3 residues within 4Å: Chain C: F.4, L.483 Ligands: HEX.48 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.4, C:L.483 pi-Cation interactions: C:F.4

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: G.51, D.276, W.754, G.755, M.774 Chain C: G.221, T.222 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.222 Water bridges: A:R.780 GOL.11: 5 residues within 4Å: Chain A: R.699, N.700, E.722 Chain E: R.23, W.57 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:R.699, A:N.700, A:E.722, E:R.23 Water bridges: A:E.722, A:E.722, A:D.723, E:R.23 GOL.25: 6 residues within 4Å: Chain B: Q.124, R.239, Y.758, N.760, D.761 Chain C: Q.120 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.124, B:R.239, B:D.761, B:D.761, C:Q.120 GOL.26: 5 residues within 4Å: Chain A: R.168, E.309 Chain B: L.75, M.76, N.820 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:L.75, B:N.820, A:R.168, A:E.309 Water bridges: B:N.820, A:R.168 GOL.27: 5 residues within 4Å: Chain A: P.223 Chain B: W.187, E.269, Y.275, A.777 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.269, B:A.777 GOL.43: 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 GOL.44: 7 residues within 4Å: Chain C: D.566, E.567, D.568, K.643, 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.45: 5 residues within 4Å: Chain B: P.223 Chain C: W.187, E.269, E.776, A.777 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.777, C:R.780 GOL.46: 5 residues within 4Å: Chain C: T.243, E.244, G.247, R.263, I.268 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.244 GOL.59: 4 residues within 4Å: Chain B: S.806 Chain D: N.122, D.143, I.152 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:N.122, B:S.806, B:S.806 GOL.60: 4 residues within 4Å: Chain A: Y.811 Chain E: E.20, R.23, D.44 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.23, E:D.44, A:Y.811

9 x HEX: HEXANE(Non-covalent)(Non-functional Binders)

HEX.12: 4 residues within 4Å: Chain A: A.457, F.458, R.468 Ligands: PTY.54 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.458 HEX.28: 1 residues within 4Å: Ligands: PTY.53 No protein-ligand interaction detected (PLIP) HEX.29: 2 residues within 4Å: Chain B: F.4, F.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.4, B:F.4, B:F.5 HEX.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.31: 1 residues within 4Å: Chain B: G.539 No protein-ligand interaction detected (PLIP) HEX.47: 3 residues within 4Å: Chain C: V.341, I.390 Ligands: D12.57 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.341, C:I.390 HEX.48: 2 residues within 4Å: Chain C: M.1 Ligands: DDQ.42 No protein-ligand interaction detected (PLIP) HEX.49: 3 residues within 4Å: Chain C: Q.439, L.486 Ligands: PTY.53 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.486 HEX.50: 1 residues within 4Å: Ligands: PTY.54 No protein-ligand interaction detected (PLIP)

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

OCT.13: 3 residues within 4Å: Chain A: S.523, S.530 Ligands: LMT.4 No protein-ligand interaction detected (PLIP) OCT.14: 1 residues within 4Å: Ligands: D10.5 No protein-ligand interaction detected (PLIP) OCT.32: 5 residues within 4Å: Chain B: L.353, Y.356, L.357, F.513, L.984 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.356, B:L.357, B:F.513, B:L.984 OCT.33: 6 residues within 4Å: Chain B: A.22, A.26, K.29, A.384 Ligands: DDQ.23, PTY.51 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.26, B:A.384

1 x FUA: FUSIDIC ACID(Non-covalent)

FUA.15: 9 residues within 4Å: Chain B: G.24, L.28, L.300, K.334, I.337, H.338, V.341, L.377 Ligands: LMT.16 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.28, B:L.300, B:I.337, B:L.377 Salt bridges: B:H.338, B:H.338

4 x D12: DODECANE(Non-covalent)

D12.34: 6 residues within 4Å: Chain B: F.885, W.895, S.896, F.899, F.1033 Ligands: D10.18 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.885, B:W.895, B:F.899, B:F.1033 D12.55: 1 residues within 4Å: Chain C: W.13 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.13 D12.56: 4 residues within 4Å: Chain C: S.523, H.526, Y.527 Ligands: LMT.36 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:H.526, C:Y.527 D12.57: 5 residues within 4Å: Chain C: G.24, A.27, L.28, L.30 Ligands: HEX.47 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.27

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

DDR.35: 16 residues within 4Å: Chain B: V.452, P.455, M.456, F.459, Y.467, M.552, Y.877, S.880, V.884, V.905, V.909, Q.928, L.931, L.932, I.935 Ligands: DDQ.24 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.452, B:Y.877, B:V.884, B:V.905, B:V.905, B:V.909, B:L.931, B:L.932, B:I.935 Hydrogen bonds: B:Y.467, B:Y.877

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.51: 11 residues within 4Å: Chain B: K.29 Chain C: A.451, V.454, P.455, F.458, S.875, V.883, C.887 Ligands: DDQ.23, OCT.33, PTY.53 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.451, C:V.454, C:P.455, C:F.458, C:F.458, C:F.458, C:V.883, B:K.29 Hydrogen bonds: C:S.875 Salt bridges: B:K.29 PTY.52: 9 residues within 4Å: Chain B: W.13, I.17, L.21 Chain C: S.894, W.895, S.896, K.950, R.1030, F.1033 14 PLIP interactions: 2 interactions with chain B, 12 interactions with chain C Hydrophobic interactions: B:W.13, B:I.17, C:W.895, C:W.895, C:W.895, C:W.895 Hydrogen bonds: C:S.894, C:W.895, C:S.896, C:K.950, C:K.950, C:R.1030, C:R.1030 Salt bridges: C:K.950 PTY.53: 14 residues within 4Å: Chain B: R.8, F.11 Chain C: G.440, V.443, M.447, C.887, A.890, L.891, Y.892, E.893, D.951 Ligands: HEX.28, HEX.49, PTY.51 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.11, B:F.11, C:V.443, C:A.890 Salt bridges: B:R.8 Hydrogen bonds: C:D.951 PTY.54: 6 residues within 4Å: Chain C: A.381, A.384, A.385, G.387 Ligands: HEX.12, HEX.50 No protein-ligand interaction detected (PLIP)

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

SO4.58: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tam, H.K. et al., Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB. J.Mol.Biol. (2020)

Release Date

2019-11-13

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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