SMTL ID : 6zog.1

Minocycline binding to the deep binding pocket of AcrB-I38F_I671T

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 9 residues within 4Å: Chain A: S.530, G.533, I.534, R.536, S.537, Y.541, L.544, L.1017, F.1020 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.544, A:L.1017, A:F.1020, A:F.1020, A:F.1020 Hydrogen bonds: A:R.536, A:Y.541 LMT.3: 10 residues within 4Å: Chain A: I.27, L.28, V.32, H.338, V.341, I.348, P.373, L.377, F.380 Ligands: 8K6.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.27, A:V.341, A:V.341, A:I.348, A:P.373, A:L.377, A:F.380, A:F.380 LMT.5: 9 residues within 4Å: Chain A: F.4, R.8, F.11, I.18 Chain B: G.440, V.443, G.444, C.887, A.890 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.11, A:F.11, A:I.18, B:V.443, B:A.890 Hydrogen bonds: A:R.8 LMT.6: 8 residues within 4Å: Chain A: G.440, G.444, C.887, A.890, L.891 Chain C: R.8, F.11, I.18 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.11, C:I.18, A:A.890 Hydrogen bonds: C:R.8, A:G.440 LMT.7: 8 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, F.1020 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.1020, B:F.1020 Hydrogen bonds: B:R.536, B:S.537, B:S.537, B:R.540, B:Y.541 LMT.18: 9 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541, I.548, F.1021 Ligands: D10.19 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.548, C:F.1021 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:Y.541

2 x D10: DECANE(Non-covalent)

D10.2: 2 residues within 4Å: Chain A: I.882, W.895 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.882, A:W.895, A:W.895, A:W.895 D10.19: 4 residues within 4Å: Chain C: S.523, H.526, Y.527 Ligands: LMT.18 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:H.526

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

EDO.4: 5 residues within 4Å: Chain A: K.55, G.691, H.692 Chain C: I.763, G.766 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.55, A:H.692 EDO.14: 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, B:K.498 EDO.22: 6 residues within 4Å: Chain C: R.185, E.273, N.274, G.755, G.756, Y.772 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.185 Water bridges: C:Y.772, C:Y.772 EDO.23: 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:E.269, C:A.777 EDO.30: 4 residues within 4Å: Chain A: T.696, D.723 Chain E: R.23, W.57 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.23, E:R.23, A:D.723 EDO.31: 3 residues within 4Å: Chain A: Y.811 Chain E: 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 DDR: (2S)-3-hydroxypropane-1,2-diyl didecanoate(Non-covalent)

DDR.8: 15 residues within 4Å: Chain B: V.452, M.456, F.459, Y.467, M.552, F.556, Y.877, S.880, L.881, V.884, V.905, Q.928, L.931, L.932, I.935 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:L.931, B:L.932, B:I.935 Hydrogen bonds: B:Y.467, B:Y.877

1 x MYS: PENTADECANE(Non-covalent)

MYS.9: 3 residues within 4Å: Chain A: L.21 Chain B: I.882, W.895 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.21, B:I.882, B:W.895

1 x 8K6: Octadecane(Non-covalent)

8K6.10: 7 residues within 4Å: Chain A: K.29 Chain B: A.451, V.454, F.458, S.875, L.876 Ligands: LMT.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.458, B:F.458, B:L.876

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.11: 10 residues within 4Å: Chain B: S.48, F.178, G.179, S.180, E.273, N.274, D.276, I.277, A.279, R.620 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.178, B:A.279 Hydrogen bonds: B:S.48, B:N.274, B:D.276, B:D.276, B:R.620, B:R.620 Salt bridges: B:E.273

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 6 residues within 4Å: Chain A: R.168, E.309 Chain B: L.75, M.76, Y.77, N.820 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.168, A:R.168, A:E.309, B:M.78 GOL.24: 5 residues within 4Å: Chain C: P.36, T.37, F.388, S.389, Q.469 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.37, C:T.37, C:S.389, C:S.389, C:Q.469 GOL.25: 7 residues within 4Å: Chain C: D.566, E.567, D.568, K.643, G.994, G.996, S.997 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.567, C:D.568, C:D.568, C:G.996 Water bridges: C:K.643, C:G.994 GOL.26: 2 residues within 4Å: Chain C: E.339, K.342 No protein-ligand interaction detected (PLIP) GOL.29: 5 residues within 4Å: Chain B: S.806 Chain D: N.122, D.143, K.147, 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

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

OCT.13: 2 residues within 4Å: Chain B: I.337, I.390 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.337, B:I.390

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

SO4.15: 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 SO4.16: 4 residues within 4Å: Chain B: K.55, G.691, H.692, E.693 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.692 Salt bridges: B:K.55 SO4.28: 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

1 x D12: DODECANE(Non-covalent)

D12.17: 2 residues within 4Å: Chain A: W.895 Chain C: W.13 No protein-ligand interaction detected (PLIP)

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.20: 14 residues within 4Å: Chain B: I.10, W.13, I.17, M.20, L.21 Chain C: A.878, I.882, F.885, E.893, S.894, W.895, S.896, F.1033, S.1034 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:W.13, B:W.13, B:I.17, B:L.21, C:A.878, C:I.882, C:F.885, C:W.895, C:W.895, C:W.895 Hydrogen bonds: C:E.893, C:S.894, C:W.895, C:S.896

1 x C14: TETRADECANE(Non-covalent)

C14.21: 3 residues within 4Å: Chain C: F.458, F.459, G.460 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458, C:F.459

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

DDQ.27: 2 residues within 4Å: Chain C: R.468, S.471 No protein-ligand interaction detected (PLIP)

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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