SMTL ID : 6zoh.1

3-Formylrifamycin SV binding to the access pocket of AcrB-G619P_G621P L and T protomers

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 9 residues within 4Å: Chain A: S.530, G.533, R.536, S.537, R.540, Y.541, L.544, L.1017, F.1020 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.544, A:L.1017, A:F.1020, A:F.1020 Hydrogen bonds: A:R.536, A:S.537, A:S.537, A:R.540, A:Y.541 LMT.2: 9 residues within 4Å: Chain A: I.27, L.28, K.29, V.32, V.341, I.348, P.373, F.380, I.390 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.341, A:V.341, A:I.348, A:P.373, A:F.380, A:I.390 Hydrogen bonds: A:K.29, A:K.29 LMT.11: 10 residues within 4Å: Chain A: G.440, G.444, C.887, A.890, L.891 Chain C: F.4, R.8, F.11, I.18 Ligands: D12.23 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.11, C:F.11, C:I.18, C:I.18, A:A.890 Salt bridges: C:R.8 Hydrogen bonds: A:G.440 LMT.13: 9 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, V.1016, F.1020 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.534, B:V.1016, B:F.1020 Hydrogen bonds: B:R.536, B:S.537, B:S.537, B:R.540, B:Y.541 LMT.21: 10 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541, L.544, I.548, F.1020, F.1021 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.548, C:F.1020, C:F.1021 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:S.537, C:R.540, C:R.540, C:Y.541 LMT.32: 8 residues within 4Å: Chain A: F.458 Chain C: A.22, A.26, K.29, A.381, A.384, A.385 Ligands: LPX.25 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.22 Hydrogen bonds: C:K.29 LMT.33: 4 residues within 4Å: Chain C: G.511, F.512, W.515, R.518 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.515, C:W.515

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

EDO.3: 5 residues within 4Å: Chain A: E.130, K.163, S.167, D.174, V.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.163, A:S.167, A:S.167, A:D.174, A:V.175 EDO.7: 3 residues within 4Å: Chain A: D.745, R.792, A.793 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.793 EDO.9: 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.12: 4 residues within 4Å: Chain A: L.782 Chain C: Q.228, Q.229, L.230 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain B: N.189, E.192, R.263, D.264 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.189 EDO.16: 6 residues within 4Å: Chain B: F.727, P.783, I.786, S.805, S.806, S.807 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.783, B:S.805, B:S.807 EDO.26: 5 residues within 4Å: Chain C: G.675, T.676, A.677, N.719, E.826 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.676, C:A.677, C:N.719 EDO.27: 6 residues within 4Å: Chain C: Q.89, T.91, S.132, S.133, S.134, K.292 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.89, C:T.91, C:S.132, C:K.292, C:K.292 EDO.28: 6 residues within 4Å: Chain A: Q.67, L.117 Chain C: Q.181, Y.758, V.768, K.770 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.181, C:V.768 EDO.29: 4 residues within 4Å: Chain C: E.339, K.342, T.993, G.994 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.342

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: P.50, R.185, E.273, N.274, G.755, G.756, Y.772, M.774 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.185, A:R.185, A:E.273, A:G.755 GOL.15: 8 residues within 4Å: Chain A: A.165, R.168, T.169, E.309 Chain B: L.75, M.76, Y.77, N.820 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.75, A:R.168 GOL.31: 6 residues within 4Å: Chain C: R.185, E.273, G.755, G.756, Y.772, M.774 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.185, C:R.185 GOL.35: 5 residues within 4Å: Chain C: E.593, H.596, Y.597, K.601, A.654 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.593, C:H.596, C:Y.597, C:K.601

4 x D12: DODECANE(Non-covalent)

D12.5: 6 residues within 4Å: Chain A: A.457, F.458, F.459, G.460, R.468, I.472 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.458, A:I.472 D12.8: 2 residues within 4Å: Chain A: W.13 Chain B: W.895 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.13 D12.22: 3 residues within 4Å: Chain C: P.455, F.458, I.879 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.879 D12.23: 3 residues within 4Å: Chain C: M.1, F.4 Ligands: LMT.11 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.4, C:F.4

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

DDQ.6: 2 residues within 4Å: Chain A: G.511, R.518 No protein-ligand interaction detected (PLIP) DDQ.18: 8 residues within 4Å: Chain A: F.11 Chain B: Q.439, G.440, V.443, G.444, M.447, C.887, A.890 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.443, B:A.890, A:F.11, A:F.11

2 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.10: 14 residues within 4Å: Chain A: M.575, Q.577, F.617, R.620, M.662, F.664, F.666, R.717, P.718, N.719, G.720, L.721, R.815, L.828 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Q.577, A:F.617, A:F.617, A:F.664, A:F.664, A:F.666, A:R.717, A:L.721, A:L.828 Hydrogen bonds: A:Q.577, A:R.620, A:R.717, A:R.717, A:N.719, A:N.719, A:N.719 Salt bridges: A:R.717 pi-Stacking: A:F.617 3YI.19: 13 residues within 4Å: Chain B: M.573, M.575, F.617, R.620, F.666, P.669, V.672, R.717, N.719, G.720, L.721, R.815, L.828 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.617, B:F.666, B:V.672, B:L.721 Hydrogen bonds: B:R.620, B:R.717, B:R.717, B:N.719, B:N.719, B:N.719 Salt bridges: B:R.717

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, 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:L.881, B:V.884, B:V.905, B:I.935, B:I.935 Hydrogen bonds: B:Y.467

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.20: 11 residues within 4Å: Chain B: W.13, M.20, L.21 Chain C: I.879, I.882, F.885, S.894, W.895, S.896, K.950, R.1030 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.879, C:I.882, C:I.882, C:F.885, C:W.895, C:W.895, B:W.13, B:L.21 Hydrogen bonds: C:W.895, C:S.896, C:K.950

1 x D10: DECANE(Non-covalent)

D10.24: 5 residues within 4Å: Chain C: M.552, F.556, V.557, Y.877, I.935 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.556, C:F.556, C:F.556, C:V.557, C:Y.877, C:I.935

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

LPX.25: 9 residues within 4Å: Chain C: V.382, G.387, F.388, R.468, Q.469, S.471, I.472, S.476 Ligands: LMT.32 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.382 Hydrogen bonds: C:G.387, C:Q.469 Salt bridges: C:R.468

2 x HEX: HEXANE(Non-covalent)

HEX.30: 1 residues within 4Å: Chain C: F.380 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.380 HEX.34: 4 residues within 4Å: Chain C: S.523, Y.527, S.530, F.1020 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.527, C:F.1020

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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