SMTL ID : 6zo7.1

3-Formylrifamycin SV binding to the access pocket of AcrB-G619P L and T protomer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 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.18 Ligands: D12.21 7 PLIP interactions: 5 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, C:R.8, A:G.440 Salt bridges: C:R.8 LMT.2: 6 residues within 4Å: Chain A: I.27, L.28, V.32, V.341, P.373, F.380 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.27, A:I.27, A:V.32, A:V.341, A:F.380, A:F.380 LMT.3: 9 residues within 4Å: Chain A: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.544, F.1020 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.544, A:L.544, A:F.1020, A:F.1020 Hydrogen bonds: A:R.536, A:S.537, A:S.537, A:R.540 LMT.6: 10 residues within 4Å: Chain A: Y.467, F.556, F.563, N.871, A.873, Y.877, L.881, N.923, Q.928, I.935 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.877, A:L.881 Hydrogen bonds: A:Y.467, A:N.871, A:N.871, A:N.923, A:Q.928 LMT.10: 10 residues within 4Å: Chain A: R.8, F.11, I.15, I.18 Chain B: Q.439, G.440, M.447, C.887, A.890, 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.15, A:I.18, B:A.890, B:L.891 LMT.12: 9 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.544, F.1020 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.544, B:F.1020 Hydrogen bonds: B:R.536, B:R.540, B:Y.541 Salt bridges: B:R.540 LMT.15: 5 residues within 4Å: Chain B: K.510, G.511, F.512, W.515, R.518 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.510 LMT.20: 8 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541, I.548, F.1021 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.548, C:I.548, C:F.1021 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:S.537, C:Y.541 LMT.23: 7 residues within 4Å: Chain C: E.339, K.342, A.635, I.991, S.992, T.993, G.994 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.993, C:T.993 Salt bridges: C:K.342 LMT.30: 4 residues within 4Å: Chain C: G.511, F.512, W.515, R.518 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.515 Hydrogen bonds: C:G.511, C:R.518

1 x D10: DECANE(Non-covalent)

D10.4: 2 residues within 4Å: Chain A: W.895 Ligands: D12.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.895, A:W.895

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

EDO.5: 7 residues within 4Å: Chain A: Y.758, D.761, V.768, K.770 Chain B: V.64, Q.67, L.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.758, A:K.770 EDO.7: 5 residues within 4Å: Chain A: N.231, S.233 Chain B: S.84, T.724, P.814 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.724, B:T.724 Water bridges: B:G.581 EDO.8: 5 residues within 4Å: Chain A: Q.124, Y.758, V.759, N.760, D.761 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.124, A:D.761, A:D.761 EDO.11: 3 residues within 4Å: Chain A: D.73, N.74 Chain C: T.295 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.295, A:N.74 EDO.16: 4 residues within 4Å: Chain B: H.525, T.528, L.965, R.969 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.525 EDO.27: 3 residues within 4Å: Chain C: D.153, D.156, R.765 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.153, C:D.156, C:R.765 EDO.31: 5 residues within 4Å: Chain B: P.223 Chain C: W.187, E.269, E.776, A.777 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.269, C:A.777, C:R.780 EDO.34: 2 residues within 4Å: Chain E: D.143, K.147 No protein-ligand interaction detected (PLIP)

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.9: 13 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, R.815, L.828 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Q.577, A:Q.577, A:F.617, A:F.617, A:F.664, A:F.664, A:F.666, A:R.717, A:L.828 Hydrogen bonds: A:R.620, A:R.717, A:R.717, A:N.719, A:N.719, A:N.719 Salt bridges: A:R.717 3YI.17: 17 residues within 4Å: Chain B: M.573, M.575, G.616, F.617, R.620, F.664, F.666, L.668, P.669, V.672, R.717, P.718, N.719, G.720, L.721, R.815, L.828 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.617, B:F.617, B:F.617, B:F.617, B:F.664, B:F.666, B:F.666, B:L.668, B:V.672, B:R.717, 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 8 residues within 4Å: Chain B: Q.124, R.239, Y.758, N.760, D.761 Chain C: P.119, Q.120, E.121 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.124, B:R.239, B:Y.758, B:D.761, B:D.761, C:Q.120, C:E.121 GOL.28: 7 residues within 4Å: Chain A: G.51, W.754, G.755, M.774 Chain C: Q.218, G.221, T.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.51 GOL.33: 5 residues within 4Å: Chain A: Y.811 Chain E: E.20, R.23, D.44, L.53 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:Y.811, E:R.23, E:R.23

1 x HEX: HEXANE(Non-covalent)

HEX.14: 2 residues within 4Å: Chain B: F.4, F.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.4, B:F.5

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

SO4.18: 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 Salt bridges: B:K.498

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.19: 9 residues within 4Å: Chain B: I.10, W.13, M.20, L.21 Chain C: S.894, W.895, S.896, K.950, S.1034 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:W.13, B:W.13, B:L.21, C:W.895, C:W.895, C:W.895 Hydrogen bonds: C:W.895, C:S.896 PTY.24: 13 residues within 4Å: Chain B: F.4, R.8, F.11, I.18 Chain C: Q.439, G.440, V.443, M.447, A.890, L.891, Y.892, K.950, D.954 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:Q.439, C:V.443, C:V.443, C:A.890, C:L.891, B:F.4, B:F.11, B:F.11, B:I.18 Hydrogen bonds: C:K.950, C:D.954 Water bridges: C:D.951 Salt bridges: B:R.8

2 x D12: DODECANE(Non-covalent)

D12.21: 2 residues within 4Å: Chain C: F.4 Ligands: LMT.1 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.4 D12.22: 3 residues within 4Å: Chain A: W.895 Chain C: W.13 Ligands: D10.4 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.13, C:W.13

1 x R16: HEXADECANE(Non-covalent)

R16.25: 4 residues within 4Å: Chain B: K.29 Chain C: F.458, S.875, V.883 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458, C:V.883

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

CL.26: 2 residues within 4Å: Chain C: N.231, S.233 Ligand excluded by PLIP

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

DDQ.29: 5 residues within 4Å: Chain C: F.388, A.457, R.468, S.471, V.475 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.388, C:A.457, C:V.475

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

NA.32: 4 residues within 4Å: Chain C: F.358, L.359, Q.360, R.973 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.517, C:R.973

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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