SMTL ID : 6zoc.1

Erythromycin binding to the access pocket of AcrB-G616P L protomer and 3-formylrifamycin SV binding to the access pocket of AcrB-G616P T protomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-3-2-mer

Ligands

2 x C14: TETRADECANE(Non-covalent)

C14.1: 11 residues within 4Å: Chain A: I.27, L.28, L.30, V.32, I.337, H.338, V.341, L.344, F.380, I.390, M.395 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.27, A:V.341, A:V.341, A:F.380, A:F.380, A:I.390 C14.24: 7 residues within 4Å: Chain B: K.29 Chain C: V.454, P.455, F.458, F.459, G.460, Q.872 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.454, C:P.455, C:F.458, C:F.458, C:Q.872

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

LMT.2: 11 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, I.19 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:M.447, A:A.890, C:F.11, C:I.15, C:I.18, C:I.18, C:I.19 Hydrogen bonds: A:G.440, C:R.8, C:R.8 LMT.13: 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 Hydrophobic interactions: B:F.1020 Hydrogen bonds: B:R.536, B:S.537, B:R.540, B:Y.541 LMT.17: 10 residues within 4Å: Chain B: I.27, N.298, L.300, D.301, K.334, I.337, V.341, L.377, F.380, I.390 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.27, B:I.27, B:I.337, B:L.377, B:F.380, B:F.380, B:I.390 Hydrogen bonds: B:N.298, B:N.298, B:D.301 LMT.22: 11 residues within 4Å: Chain C: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.544, I.547, I.548, L.1017 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.544, C:L.544, C:I.547, C:I.548, C:L.1017 Hydrogen bonds: C:R.536, C:R.536, C:R.540, C:Y.541 LMT.29: 7 residues within 4Å: Chain A: F.458 Chain C: I.19, A.26, K.29, A.384, A.385, L.480 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.19, C:A.385, C:L.480 Hydrogen bonds: C:K.29

1 x ERY: ERYTHROMYCIN A(Non-covalent)

ERY.3: 18 residues within 4Å: Chain A: S.79, N.81, S.134, S.135, F.136, K.292, M.573, F.615, P.616, L.668, V.672, E.673, D.681, E.683, N.719, E.826, G.861, M.862 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.136, A:F.615, A:P.616, A:P.616, A:L.668, A:V.672, A:E.673 Hydrogen bonds: A:S.134, A:K.292, A:K.292, A:E.673, A:N.719 Salt bridges: A:E.683, A:E.826

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

EDO.4: 8 residues within 4Å: Chain A: Q.218, N.231, A.232, S.233 Chain B: S.84, N.623, T.724, P.814 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.724 EDO.5: 4 residues within 4Å: Chain A: S.530, G.533, I.534, Y.541 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: I.278, Q.584, E.585, Q.588 Chain C: K.226 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.584 EDO.9: 7 residues within 4Å: Chain A: A.165, R.168, E.309 Chain B: L.75, M.76, Y.77, N.820 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.76, B:N.820, A:R.168 EDO.12: 5 residues within 4Å: Chain A: N.744 Chain C: T.205, K.208, A.209 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.744 EDO.14: 8 residues within 4Å: Chain B: Q.124, R.239, Y.758, N.760, D.761 Chain C: P.119, Q.120, E.121 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.124, B:R.239, B:D.761, C:Q.120 EDO.28: 3 residues within 4Å: Chain C: P.224, V.225, K.226 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.226 EDO.30: 6 residues within 4Å: Chain C: S.46, A.47, S.48, Q.125, G.126, S.128 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.126, C:S.128, C:S.128 EDO.31: 6 residues within 4Å: Chain C: V.557, L.559, P.560, S.561, E.839, E.842 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.561 EDO.32: 3 residues within 4Å: Chain C: D.745, R.792, A.793 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.792, C:R.792, C:R.792 EDO.33: 9 residues within 4Å: Chain C: S.134, S.135, F.136, M.573, F.615, P.616, I.626, F.628, T.676 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.136 EDO.37: 3 residues within 4Å: Chain E: D.72, A.75, Y.76 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.76, E:Y.76

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: P.50, R.185, E.273, N.274, Y.275, G.755, G.756, Y.772, M.774 Chain C: T.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.185, A:R.185, A:N.274, A:G.755 GOL.7: 9 residues within 4Å: Chain A: D.566, E.567, D.568, W.634, K.643, G.994, S.997, G.998, N.1001 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.566, A:E.567, A:K.643, A:G.998 GOL.11: 9 residues within 4Å: Chain A: I.743, N.744, N.747 Chain C: K.208, A.209, A.212, V.214, Q.237 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.744 GOL.26: 8 residues within 4Å: Chain A: A.688, G.689 Chain C: A.160, N.161, D.764, R.765, R.767, K.769 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:G.689 Hydrogen bonds: C:R.765, C:K.769 GOL.27: 8 residues within 4Å: Chain A: L.75, M.76, N.820 Chain C: D.164, A.165, R.168, T.169, E.309 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.165, C:R.168, C:E.309

2 x D12: DODECANE(Non-covalent)

D12.10: 4 residues within 4Å: Chain A: W.895 Chain C: I.10, W.13, I.17 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.10, C:W.13, C:I.17 D12.18: 10 residues within 4Å: Chain A: F.4, R.8, F.11 Chain B: G.440, V.443, G.444, M.447, C.887, A.890, L.891 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.11, A:F.11, A:F.11, B:L.891

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

OCT.15: 6 residues within 4Å: Chain B: M.1, F.4, F.5, F.11, I.15, I.487 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.4, B:F.4, B:F.5 OCT.23: 7 residues within 4Å: Chain C: M.1, Q.439, V.443, V.482, L.483, L.486 Ligands: HEX.35 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.482, C:L.486

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

HEX.16: 9 residues within 4Å: Chain B: V.452, M.456, F.459, Y.467, L.876, Y.877, S.880, Q.928, L.932 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:M.456, B:Y.877, B:Y.877, B:L.932 HEX.35: 6 residues within 4Å: Chain C: Q.439, V.443, M.447, L.891 Ligands: DDQ.20, OCT.23 No protein-ligand interaction detected (PLIP)

1 x 3YI: (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptam ethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate(Non-covalent)

3YI.19: 13 residues within 4Å: Chain B: M.575, F.617, A.618, F.664, F.666, L.668, P.669, T.676, R.717, N.719, G.720, R.815, L.828 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.617, B:F.664, B:F.666, B:L.668 Hydrogen bonds: B:A.618, B:R.717, B:R.717, B:N.719, B:N.719, B:N.719 Water bridges: B:E.826 Salt bridges: B:R.717 pi-Stacking: B:F.617

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

DDQ.20: 11 residues within 4Å: Chain B: F.4, R.8, F.11, V.14, I.18 Chain C: M.447, L.886, C.887, A.890, L.891 Ligands: HEX.35 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.891, B:F.11, B:F.11, B:V.14, B:I.18 Hydrogen bonds: B:R.8

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

SO4.21: 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 SO4.36: 4 residues within 4Å: Chain B: E.693 Chain D: Y.56, W.57, F.90 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.56

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

PG4.25: 8 residues within 4Å: Chain B: R.168 Chain C: M.69, L.75, M.76, Y.77, M.78, N.820, L.822 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.168

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.34: 13 residues within 4Å: Chain B: I.10, W.13, I.17, L.21 Chain C: I.882, F.885, L.886, E.893, S.894, W.895, S.896, R.1030, F.1033 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.882, C:F.885, C:L.886, C:W.895, C:W.895, C:W.895, C:W.895, B:I.10, B:W.13, B:W.13 Hydrogen bonds: C:E.893, C:W.895, C:S.896 Salt bridges: C:R.1030

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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