SMTL ID : 6zo9.1

Binding of two rifabutins to the access pocket of AcrB-G621P T protomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-3-2-mer

Ligands

3 x D12: DODECANE(Non-covalent)

D12.1: 4 residues within 4Å: Chain A: A.457, G.460, G.461, R.468 No protein-ligand interaction detected (PLIP) D12.23: 3 residues within 4Å: Chain A: W.895 Chain C: W.13, M.20 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.13 D12.24: 2 residues within 4Å: Chain C: F.4, F.5 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.4, C:F.4, C:F.5

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

LMT.2: 8 residues within 4Å: Chain A: I.27, L.28, K.29, V.32, V.341, I.348, L.377, F.380 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.32, A:V.341, A:I.348, A:L.377, A:F.380, A:F.380 Hydrogen bonds: A:K.29 LMT.3: 10 residues within 4Å: Chain A: G.440, G.444, M.447, C.887, A.890, L.891 Chain C: R.8, F.11, I.15, I.18 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:M.447, C:F.11, C:I.15, C:I.18, C:I.18 Hydrogen bonds: A:G.440, C:R.8 LMT.4: 7 residues within 4Å: Chain A: S.530, G.533, I.534, R.536, R.540, Y.541, F.1020 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1020 Hydrogen bonds: A:R.536, A:R.540, A:Y.541 LMT.8: 8 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, F.1020 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.536, B:S.537, B:S.537, B:R.540, B:Y.541 LMT.25: 8 residues within 4Å: Chain C: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.544 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.544 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:R.540, C:Y.541 LMT.26: 5 residues within 4Å: Chain C: G.511, F.512, W.515, F.516, R.518 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.512, C:F.516 Hydrogen bonds: C:G.511, C:R.518

3 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.5: 8 residues within 4Å: Chain A: F.4, F.11, I.18 Chain B: Q.439, G.440, M.447, C.887, L.891 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:L.891 Salt bridges: A:R.8 Hydrogen bonds: B:Q.439 PTY.27: 11 residues within 4Å: Chain B: W.13, I.17, L.21 Chain C: I.882, F.885, S.894, W.895, S.896, K.950, R.1030, S.1034 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.882, C:I.882, C:F.885, C:W.895, C:W.895, C:W.895, C:W.895, B:W.13, B:I.17, B:L.21 Hydrogen bonds: C:S.894, C:W.895, C:S.896, C:S.896, C:K.950, C:K.950, C:R.1030 Salt bridges: C:K.950 PTY.28: 12 residues within 4Å: Chain B: R.8, F.11, I.18 Chain C: Q.439, G.440, M.447, A.890, L.891, Y.892, E.947, K.950, D.951 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.11, B:F.11, B:I.18, C:A.890 Salt bridges: B:R.8 Hydrogen bonds: C:E.947

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: Y.811 Chain E: K.16, E.20, R.23, D.44 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:K.16, E:E.20, E:D.44, A:Y.811 Water bridges: E:K.16 GOL.13: 9 residues within 4Å: Chain A: A.165, R.168, T.169, E.309 Chain B: L.75, M.76, Y.77, M.78, N.820 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.168, A:E.309, B:M.78 GOL.31: 7 residues within 4Å: Chain C: S.562, L.564, P.565, D.566, S.836, T.837, T.922 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.562, C:D.566, C:D.566, C:T.837 Water bridges: C:D.566

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

EDO.7: 3 residues within 4Å: Chain A: P.36, T.37, S.389 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.37, A:S.389 Water bridges: A:N.391 EDO.15: 5 residues within 4Å: Chain B: S.233 Chain C: S.84, P.621, T.724, P.814 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.84, C:N.623, B:S.233, B:S.233 EDO.16: 4 residues within 4Å: Chain B: T.463, Y.467, E.866, S.869 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.467 Water bridges: B:E.866 EDO.17: 5 residues within 4Å: Chain A: F.316, F.317 Chain B: A.688, T.853, G.854 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.854

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

DDR.9: 15 residues within 4Å: Chain B: V.452, P.455, M.456, F.459, Y.467, M.552, F.556, Y.877, S.880, L.881, V.884, V.905, Q.928, L.932, I.935 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.556, B:L.881, B:V.884, B:V.905, B:I.935 Hydrogen bonds: B:Y.467

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

HEX.10: 1 residues within 4Å: Chain B: W.895 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.895, B:W.895 HEX.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

OCT.11: 3 residues within 4Å: Chain B: L.300, I.337, I.390 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.300, B:I.337, B:I.390 OCT.12: 3 residues within 4Å: Chain B: F.885, F.899, M.902 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.885, B:F.885, B:F.899, B:F.899 OCT.30: 1 residues within 4Å: Chain C: S.530 No protein-ligand interaction detected (PLIP)

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

SO4.14: 3 residues within 4Å: Chain B: K.55, G.691, H.692 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.692 Salt bridges: B:K.55 SO4.32: 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

2 x RBT: RIFABUTIN(Non-covalent)

RBT.18: 20 residues within 4Å: Chain B: M.575, Q.577, A.618, F.664, F.666, T.676, T.678, G.679, F.680, D.681, S.715, R.717, P.718, N.719, G.720, E.826, L.828, G.829, Q.830 Ligands: RBT.19 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Q.577, B:A.618, B:F.664, B:F.666, B:L.828, B:L.828 Hydrogen bonds: B:T.676, B:S.715, B:R.717, B:N.719, B:Q.830 pi-Stacking: B:F.666, B:F.666 RBT.19: 14 residues within 4Å: Chain B: S.135, M.575, F.617, A.618, F.666, P.669, V.672, E.673, L.674, G.675, N.719, R.815, M.862 Ligands: RBT.18 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.617, B:F.617, B:F.666, B:L.674 Hydrogen bonds: B:N.719, B:R.815 pi-Stacking: B:F.617

1 x C14: TETRADECANE(Non-covalent)

C14.20: 1 residues within 4Å: Chain C: F.458 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.458

2 x D10: DECANE(Non-covalent)

D10.21: 4 residues within 4Å: Chain C: A.553, F.556, V.909, I.935 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.553, C:F.556, C:V.909, C:I.935 D10.22: 1 residues within 4Å: Chain C: F.380 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.380

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

CL.33: 1 residues within 4Å: Chain C: R.468 Ligand excluded by 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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