SMTL ID : 6zo6.1

Minocycline binding to the deep binding pocket of AcrB-G619P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 10 residues within 4Å: Chain A: I.27, L.28, V.32, I.337, H.338, V.341, I.348, P.373, F.380 Ligands: 8K6.48 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.27, A:I.337, A:V.341, A:I.348, A:P.373, A:F.380, A:F.380 LMT.2: 9 residues within 4Å: Chain A: G.440, G.444, C.887, A.890, L.891 Chain C: R.8, F.11, I.15, I.18 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.11, C:I.15, C:I.18 Hydrogen bonds: C:R.8, C:R.8, A:G.440 LMT.3: 11 residues within 4Å: Chain A: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.544, L.1017, F.1020, F.1021 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.544, A:F.1020, A:F.1020, A:F.1021 Hydrogen bonds: A:R.536, A:R.536, A:R.540, A:R.540, A:Y.541 LMT.19: 10 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.544, F.1020 Ligands: D10.24 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.544, B:F.1020 Hydrogen bonds: B:S.530, B:R.536, B:S.537, B:S.537, B:R.540, B:Y.541 LMT.20: 7 residues within 4Å: Chain B: G.508, K.509, K.510, G.511, F.512, W.515, R.518 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.510 Hydrogen bonds: B:R.518 Water bridges: B:F.512 LMT.52: 11 residues within 4Å: Chain C: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, I.548, F.1020, F.1021 Ligands: DDQ.56 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.548, C:F.1020, C:F.1020, C:F.1021 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:S.537, C:Y.541

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

OCT.4: 3 residues within 4Å: Chain A: F.458, R.468 Ligands: DDQ.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.458 OCT.54: 3 residues within 4Å: Chain C: I.337, V.341, F.380 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.337, C:V.341, C:F.380 OCT.55: 4 residues within 4Å: Chain C: A.457, F.458, R.468 Ligands: LPX.69 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.458

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

DDQ.5: 5 residues within 4Å: Chain A: F.386, F.388, R.468, I.472 Ligands: OCT.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.386, A:F.386, A:F.386, A:F.388, A:I.472 DDQ.22: 6 residues within 4Å: Chain A: F.4 Chain B: G.440, M.447, C.887, A.890, L.891 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.891 DDQ.23: 4 residues within 4Å: Chain A: W.13, I.17 Chain B: W.895 Ligands: MYS.35 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.13, A:W.13, A:W.13, A:I.17 DDQ.56: 5 residues within 4Å: Chain C: S.523, H.526, Y.527, S.530 Ligands: LMT.52 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:H.526, C:Y.527 DDQ.57: 3 residues within 4Å: Chain C: W.13, I.17 Ligands: D12.12 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.13, C:I.17

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: G.51, D.276, G.755, M.774 Chain C: Q.218, G.221, T.222 Ligands: GOL.7 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:T.222, A:G.51, A:D.276 Water bridges: C:Q.218, C:G.221, A:Y.275, A:D.276, A:R.620 GOL.7: 8 residues within 4Å: Chain A: P.50, R.185, E.273, N.274, G.755, Y.772, M.774 Ligands: GOL.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.51, A:R.185, A:R.185, A:E.273 Water bridges: A:R.620, A:R.620 GOL.8: 7 residues within 4Å: Chain A: S.46, A.47, S.48, Q.125, G.126, S.128 Ligands: EDO.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.47, A:Q.125, A:S.128, A:S.128 GOL.9: 6 residues within 4Å: Chain A: D.566, E.567, D.568, K.643, S.997, G.998 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.566, A:E.567, A:D.568 GOL.10: 5 residues within 4Å: Chain A: E.593, H.596, Y.597, K.601, A.654 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.596, A:K.601, A:A.654 GOL.11: 5 residues within 4Å: Chain A: S.742, I.743, N.744 Chain C: T.205, A.209 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.742, A:I.743, A:N.744, A:N.744 Water bridges: A:Q.737 GOL.27: 8 residues within 4Å: Chain A: A.165, R.168, E.309 Chain B: L.75, M.76, Y.77, M.78, N.820 6 PLIP interactions: 5 interactions with chain A, 1 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 GOL.28: 8 residues within 4Å: Chain B: F.358, L.359, Q.360, I.500, D.504, H.505, G.506, K.509 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.358, B:K.509 GOL.29: 5 residues within 4Å: Chain B: E.593, Y.597, A.654, F.655, I.658 No protein-ligand interaction detected (PLIP) GOL.30: 5 residues within 4Å: Chain B: Q.237, T.238, L.240, E.245 Chain C: K.728 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.238, C:K.728, C:K.728 GOL.60: 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.61: 9 residues within 4Å: Chain A: V.64, Q.67, L.117 Chain C: Q.181, Y.758, D.761, V.768, K.769, K.770 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.181, C:Y.758, C:V.768 GOL.62: 1 residues within 4Å: Chain C: W.515 No protein-ligand interaction detected (PLIP) GOL.83: 5 residues within 4Å: Chain A: Y.811 Chain E: L.19, R.23, D.44, L.53 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.23, E:R.23, E:D.44, A:Y.811

3 x D12: DODECANE(Non-covalent)

D12.12: 3 residues within 4Å: Chain A: W.895 Chain C: I.17 Ligands: DDQ.57 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.17, A:W.895, A:W.895 D12.65: 3 residues within 4Å: Chain C: F.4, F.5, I.487 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.4, C:F.4, C:F.5, C:I.487 D12.66: 2 residues within 4Å: Chain C: L.353, F.513 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.353, C:F.513, C:F.513, C:F.513

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

HEX.13: 2 residues within 4Å: Chain A: F.885, F.899 No protein-ligand interaction detected (PLIP) HEX.32: 1 residues within 4Å: Chain B: A.384 No protein-ligand interaction detected (PLIP) HEX.33: 3 residues within 4Å: Chain B: F.4, F.5 Ligands: HEX.34 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.4, B:F.4, B:F.4, B:F.5 HEX.34: 2 residues within 4Å: Ligands: D10.26, HEX.33 No protein-ligand interaction detected (PLIP) HEX.67: 3 residues within 4Å: Chain C: A.385, F.386 Ligands: LPX.69 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.386 HEX.68: 2 residues within 4Å: Chain C: L.486 Ligands: C14.51 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.486

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

EDO.14: 3 residues within 4Å: Chain A: P.36, T.37, S.389 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: S.46, S.128, E.130, D.174, Q.176 Ligands: GOL.8 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: T.243, E.244, R.263, I.268 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain B: E.693, E.810, Y.811, G.812 Chain D: Y.56, F.90 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain B: N.700 Chain D: R.23, W.57 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain A: F.316 Chain B: G.856, Y.857 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain B: R.185, E.273, N.274, G.755, Y.772, M.774 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain B: N.189, E.192, R.263, D.264, A.266 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain B: S.46, A.47, S.48, Q.125, G.126, S.128 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain B: A.421, H.505, E.521, R.973 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain A: A.209, A.212 Chain B: I.743, N.744, N.747 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain B: R.239, N.760, D.761 Chain C: Q.120, E.121 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain B: F.727, P.783, I.786, S.802, S.805, S.807 Ligand excluded by PLIP EDO.71: 4 residues within 4Å: Chain C: N.282, G.283, Q.284, P.285 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain C: E.607, S.630, L.631, K.632, D.633 Ligand excluded by PLIP EDO.73: 5 residues within 4Å: Chain C: T.44, Q.89, S.132, S.133, S.134 Ligand excluded by PLIP EDO.74: 5 residues within 4Å: Chain C: G.675, T.676, D.681, E.826, L.828 Ligand excluded by PLIP EDO.75: 3 residues within 4Å: Chain C: K.55, G.691, H.692 Ligand excluded by PLIP EDO.76: 7 residues within 4Å: Chain A: S.84, G.581, T.724 Chain C: Q.218, N.231, A.232, S.233 Ligand excluded by PLIP EDO.77: 3 residues within 4Å: Chain B: L.230 Chain C: W.809, Y.811 Ligand excluded by PLIP EDO.78: 6 residues within 4Å: Chain C: D.83, T.85, T.87, A.618, P.619, R.620 Ligand excluded by PLIP EDO.80: 5 residues within 4Å: Chain B: E.693 Chain D: Y.56, W.57, F.90, H.92 Ligand excluded by PLIP EDO.81: 4 residues within 4Å: Chain B: Y.811 Chain D: L.19, R.23, D.44 Ligand excluded by PLIP EDO.82: 2 residues within 4Å: Chain D: A.75, Y.76 Ligand excluded by PLIP

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

PGE.17: 10 residues within 4Å: Chain A: N.144, T.148, M.149, D.153, D.156, Y.157, Y.182, P.318, S.319, R.765 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.144, A:D.156, A:Y.157, A:R.765 Water bridges: A:T.148, A:S.319 PGE.79: 8 residues within 4Å: Chain B: R.168 Chain C: E.66, M.69, N.70, L.75, M.76, M.78, N.820 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.69

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.18: 11 residues within 4Å: Chain B: S.48, F.178, G.179, S.180, E.273, N.274, D.276, I.277, A.279, V.612, F.615 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.178, B:I.277, B:V.612 Hydrogen bonds: B:S.48, B:N.274, B:N.274, B:D.276, B:D.276 Water bridges: B:S.155, B:S.155, B:F.178, B:S.180, B:N.274, B:I.277

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

DDR.21: 16 residues within 4Å: Chain B: V.452, P.455, M.456, F.459, Y.467, M.552, F.556, L.876, Y.877, S.880, L.881, V.884, V.905, Q.928, L.931, L.932 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.556, B:Y.877, B:L.881, B:V.884, B:V.905, B:V.905, B:Q.928, B:L.931, B:L.932 Hydrogen bonds: B:Y.467, B:Y.877

5 x D10: DECANE(Non-covalent)

D10.24: 4 residues within 4Å: Chain B: H.526, S.530, F.1020 Ligands: LMT.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.1020 D10.25: 6 residues within 4Å: Chain B: N.298, D.301, I.337, V.341, F.380, I.390 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.337, B:V.341, B:F.380, B:I.390 D10.26: 7 residues within 4Å: Chain B: F.11 Chain C: M.447, C.887, A.890, L.891 Ligands: HEX.34, C14.51 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.890 D10.58: 6 residues within 4Å: Chain C: M.552, A.553, F.556, V.557, Y.877, V.909 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.553, C:F.556, C:F.556, C:V.557, C:Y.877, C:V.909 D10.59: 2 residues within 4Å: Chain C: A.384, A.385 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.31: 2 residues within 4Å: Chain B: G.691, H.692 Ligand excluded by PLIP CL.63: 3 residues within 4Å: Chain C: K.950, R.1030 Ligands: PTY.53 Ligand excluded by PLIP CL.64: 3 residues within 4Å: Chain C: S.537, G.539, R.540 Ligand excluded by PLIP

2 x MYS: PENTADECANE(Non-covalent)

MYS.35: 4 residues within 4Å: Chain B: I.882, F.885, W.895 Ligands: DDQ.23 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.882, B:F.885, B:W.895, B:W.895 MYS.36: 4 residues within 4Å: Chain B: F.885, W.895, F.899, F.1033 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.885, B:F.885, B:W.895, B:F.899, B:F.1033

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.37: 13 residues within 4Å: Chain A: N.109 Chain B: Q.108, Q.112, M.115, G.126, V.127 Chain C: Q.108, L.111, Q.112, M.115, P.116, V.127, V.129 6 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B, 1 interactions with chain A Water bridges: C:Q.112, C:Q.112, B:Q.112 Hydrogen bonds: B:V.127, B:V.127, A:N.109

1 x 8K6: Octadecane(Non-covalent)

8K6.48: 7 residues within 4Å: Chain B: S.450, A.451, V.454, S.875, L.876, I.879 Ligands: LMT.1 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.876, B:I.879, B:I.879

1 x R16: HEXADECANE(Non-covalent)

R16.49: 5 residues within 4Å: Chain B: K.29 Chain C: V.454, F.458, F.459, S.875 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.454, C:F.458, C:F.459, C:F.459

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

SO4.50: 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

1 x C14: TETRADECANE(Non-covalent)

C14.51: 5 residues within 4Å: Chain C: G.440, L.891, Y.892 Ligands: D10.26, HEX.68 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.891

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.53: 15 residues within 4Å: Chain B: I.10, W.13, I.17, M.20, L.21 Chain C: I.882, F.885, E.893, S.894, W.895, S.896, R.1030, F.1033, S.1034 Ligands: CL.63 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.885, C:W.895, C:W.895, C:W.895, B:W.13, B:I.17 Hydrogen bonds: C:E.893, C:W.895, C:S.896, C:S.896, C:R.1030

1 x LPX: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate(Non-covalent)

LPX.69: 14 residues within 4Å: Chain C: V.382, F.386, F.388, A.457, R.468, Q.469, S.471, I.472, V.475, S.476, L.480, L.483 Ligands: OCT.55, HEX.67 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.382, C:F.386, C:A.457, C:V.475, C:L.480, C:L.483 Water bridges: C:G.387, C:Q.469 Salt bridges: C:R.468

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.70: 13 residues within 4Å: Chain C: I.335, E.339, D.566, E.567, D.568, W.634, A.635, K.643, T.993, G.994, A.995, S.997, G.998 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.995 Water bridges: C:D.568

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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