SMTL ID : 6zo8.1

Minocycline binding to the deep binding pocket of AcrB-G621P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 10 residues within 4Å: Chain A: I.27, L.28, K.29, V.32, H.338, V.341, I.348, L.377, F.380 Ligands: C14.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.27, A:V.32, A:I.348, A:L.377, A:F.380 LMT.2: 9 residues within 4Å: Chain A: G.440, G.444, M.447, C.887, A.890, L.891 Chain C: R.8, I.15, I.18 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.15, C:I.18, C:I.18, A:A.890 Hydrogen bonds: C:R.8, A:G.440 LMT.3: 8 residues within 4Å: Chain A: S.530, G.533, I.534, R.536, S.537, Y.541, L.1017, F.1020 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1017, A:F.1020 Hydrogen bonds: A:R.536, A:R.536, A:S.537, A:S.537, A:Y.541 LMT.4: 9 residues within 4Å: Chain A: F.386, A.457, F.458, G.460, R.468, I.472, V.475 Chain C: K.29 Ligands: LMT.37 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.386, A:F.458, A:I.472, A:V.475 Hydrogen bonds: A:F.458, A:G.461 Salt bridges: A:R.468 LMT.5: 4 residues within 4Å: Chain A: M.1, N.3, Q.439 Ligands: PTY.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.1, A:N.3, A:Q.439 LMT.15: 11 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.544, L.1017, F.1020 Ligands: D10.24 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.1017 Hydrogen bonds: B:R.536, B:R.536, B:S.537, B:R.540, B:Y.541 LMT.36: 10 residues within 4Å: Chain C: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, F.1020, F.1021 Ligands: D10.50 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.1020, C:F.1021 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:Y.541 LMT.37: 6 residues within 4Å: Chain A: F.458 Chain C: K.29, A.384, A.385 Ligands: LMT.4, LPX.57 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.29, C:G.387 LMT.38: 7 residues within 4Å: Chain C: E.339, K.342, I.991, S.992, T.993, G.994 Ligands: GOL.47 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.991 Hydrogen bonds: C:H.338, C:E.339, C:T.993, C:T.993, C:G.994 Salt bridges: C:K.342

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: G.217, Q.218, G.221, T.222 Chain B: G.51, D.276, G.755, M.774 Ligands: GOL.20 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: P.50, R.185, E.273, N.274, G.755, Y.772, M.774 Ligands: GOL.41 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: R.168, E.309 Chain B: L.75, M.76, Y.77, M.78, N.820 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain B: Q.218, N.231, A.232, S.233 Chain C: S.84, P.621, Q.622, P.814 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain B: R.185, E.273, N.274, G.755, Y.772, M.774 Ligands: GOL.6 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain B: F.727, P.783, I.786, G.787, S.802, S.805, S.806, S.807 Ligand excluded by PLIP GOL.22: 2 residues within 4Å: Chain B: V.557, S.836 Ligand excluded by PLIP GOL.40: 8 residues within 4Å: Chain C: R.185, E.273, N.274, G.755, G.756, S.757, Y.772, M.774 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain A: G.51, G.755, M.774 Chain C: Q.218, G.221, T.222 Ligands: GOL.7 Ligand excluded by PLIP GOL.42: 8 residues within 4Å: Chain B: S.167, T.169, V.172 Chain C: M.69, N.70, G.71, I.72, L.75 Ligand excluded by PLIP GOL.43: 6 residues within 4Å: Chain C: M.69, N.70, L.75, Y.77, M.78, N.820 Ligand excluded by PLIP GOL.44: 3 residues within 4Å: Chain C: E.567, D.568, S.997 Ligand excluded by PLIP GOL.45: 10 residues within 4Å: Chain A: V.64, Q.67, L.117 Chain C: Q.181, E.273, Y.758, D.761, V.768, K.769, K.770 Ligand excluded by PLIP GOL.46: 2 residues within 4Å: Chain C: G.856, Y.857 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain C: P.638, G.639, K.643, T.993 Ligands: LMT.38 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain C: E.593, H.596, Y.597, A.654 Ligand excluded by PLIP

7 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.8: 1 residues within 4Å: Chain A: W.895 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.895, A:W.895, A:W.895 D10.9: 1 residues within 4Å: Chain A: W.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.13, A:W.13, A:W.13 D10.23: 4 residues within 4Å: Chain B: F.458, R.468, V.475, S.476 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.458, B:V.475 D10.24: 3 residues within 4Å: Chain B: S.523, S.530 Ligands: LMT.15 No protein-ligand interaction detected (PLIP) D10.49: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.50: 4 residues within 4Å: Chain C: S.523, H.526, Y.527 Ligands: LMT.36 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.527 D10.51: 4 residues within 4Å: Chain C: A.457, F.458, R.468 Ligands: LPX.57 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.458

2 x C14: TETRADECANE(Non-covalent)

C14.10: 6 residues within 4Å: Chain A: K.29 Chain B: V.454, S.875, L.876, I.879 Ligands: LMT.1 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.454, B:L.876, B:I.879 C14.54: 2 residues within 4Å: Chain C: V.454, F.458 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.454, C:F.458, C:F.458

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

EDO.11: 5 residues within 4Å: Chain A: K.55, G.691, H.692, E.693 Chain C: G.766 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.55, A:H.692 EDO.12: 5 residues within 4Å: Chain A: D.566, E.567, D.568, G.994, S.997 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.566, A:E.567, A:D.568, A:G.994 EDO.28: 4 residues within 4Å: Chain A: Q.218, S.233 Chain B: T.724, P.814 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.233, B:T.724 Water bridges: A:S.233, A:S.233 EDO.29: 4 residues within 4Å: Chain B: Q.726, E.810, Y.811 Chain D: Y.56 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Q.726, D:Y.56 Water bridges: B:Q.726, B:R.808, D:Y.56 EDO.30: 4 residues within 4Å: Chain B: Q.210, E.245, K.248, I.249 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.210 EDO.31: 4 residues within 4Å: Chain B: V.201, I.204, T.205, K.208 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.201 EDO.61: 7 residues within 4Å: Chain C: N.81, Q.89, G.616, F.617, A.618, N.719, R.815 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.618, C:N.719 EDO.62: 5 residues within 4Å: Chain A: G.581, T.724 Chain C: Q.218, N.231, S.233 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.581, A:T.724, A:T.724, C:Q.218, C:N.231 Water bridges: C:S.233 EDO.65: 5 residues within 4Å: Chain A: K.248 Chain D: N.122, I.152, N.155, N.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.152, D:N.155 EDO.66: 4 residues within 4Å: Chain B: Y.811 Chain D: E.20, 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.67: 2 residues within 4Å: Chain D: A.75, Y.76 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.76, D:Y.76 EDO.68: 4 residues within 4Å: Chain A: Y.811 Chain E: E.20, R.23, D.44 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Y.811, E:R.23

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.13: 11 residues within 4Å: Chain B: L.177, F.178, G.179, S.180, N.274, D.276, I.277, A.279, V.612, F.615, R.620 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.178, B:I.277, B:V.612 Hydrogen bonds: B:N.274, B:D.276, B:D.276 Water bridges: B:F.178, B:S.180, B:N.274, B:A.286

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

LMU.14: 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:F.666, B:L.668, B:V.672 Hydrogen bonds: B:D.566

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.16: 9 residues within 4Å: Chain A: F.5, F.11, I.15, L.483 Chain B: G.440, G.444, C.887, A.890 Ligands: LMT.5 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.5, A:F.11, A:I.15, A:L.483, B:A.890 PTY.39: 11 residues within 4Å: Chain B: F.4, R.8, I.18 Chain C: Q.439, G.440, V.443, A.890, L.891, Y.892, K.950, D.954 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.4, B:I.18, C:V.443, C:A.890 Salt bridges: B:R.8 Hydrogen bonds: C:D.954 Water bridges: C:E.893

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

DDR.17: 14 residues within 4Å: Chain B: V.452, P.455, M.456, F.459, Y.467, M.552, Y.877, S.880, L.881, V.884, V.905, Q.928, L.932, I.935 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.881, B:V.884, B:V.905, B:V.905, B:I.935 Hydrogen bonds: B:Y.467, B:Y.877, B:Q.928

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

OCT.25: 2 residues within 4Å: Chain B: I.337, F.380 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.337, B:F.380 OCT.52: 1 residues within 4Å: Ligands: D12.56 No protein-ligand interaction detected (PLIP) OCT.53: 2 residues within 4Å: Chain C: M.552, F.556 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.556, C:F.556

3 x D12: DODECANE(Non-covalent)

D12.26: 1 residues within 4Å: Chain B: W.895 No protein-ligand interaction detected (PLIP) D12.55: 2 residues within 4Å: Chain A: W.895 Chain C: W.13 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.13, C:W.13 D12.56: 3 residues within 4Å: Chain C: F.4, F.5 Ligands: OCT.52 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.4, C:F.4, C:F.5

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

HEX.27: 1 residues within 4Å: Chain B: V.443 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.443 HEX.59: 2 residues within 4Å: Chain C: M.902, L.903 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.903 HEX.60: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

SO4.32: 5 residues within 4Å: Chain B: R.239, N.760, D.761 Chain C: P.119, Q.120 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.761, C:Q.120 Salt bridges: B:R.239 SO4.63: 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 SO4.64: 3 residues within 4Å: Chain C: K.950, R.1030 Ligands: LPX.58 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.950, C:R.1030

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

DDQ.33: 2 residues within 4Å: Chain B: W.13 Ligands: LPX.58 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.13, B:W.13

1 x NA: SODIUM ION(Non-functional Binders)

NA.34: 2 residues within 4Å: Chain B: N.744, N.747 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.744, B:N.747 Water bridges: B:N.744

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

CL.35: 3 residues within 4Å: Chain B: N.361, F.362, K.498 Ligand excluded by PLIP

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

LPX.57: 12 residues within 4Å: Chain C: F.386, G.387, F.388, A.457, R.468, S.471, I.472, V.475, S.476, L.480 Ligands: LMT.37, D10.51 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.457, C:V.475, C:L.480 Hydrogen bonds: C:G.387 Water bridges: C:T.37, C:Q.469 Salt bridges: C:R.468 LPX.58: 10 residues within 4Å: Chain B: I.10 Chain C: I.882, F.885, E.893, S.894, W.895, S.896, S.1034 Ligands: DDQ.33, SO4.64 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.882, C:W.895 Hydrogen bonds: C:W.895, C:S.896, C:S.896

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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