SMTL ID : 6zob.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-2-mer

Ligands

6 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.15, I.18 9 PLIP interactions: 4 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, A:G.444, C:R.8 Water bridges: A:E.947 LMT.2: 7 residues within 4Å: Chain A: I.27, L.28, V.341, L.344, I.348, L.377, F.380 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.27, A:I.27, A:V.341, A:V.341, A:L.344, A:I.348, A:L.377, A:F.380 Hydrogen bonds: A:L.28 LMT.3: 8 residues within 4Å: Chain A: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, F.1020 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.534, A:F.1020 Hydrogen bonds: A:R.536, A:R.536, A:R.536, A:S.537, A:S.537, A:R.540, A:Y.541 LMT.6: 1 residues within 4Å: Chain A: G.511 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.511 LMT.10: 10 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, V.1016, L.1017, F.1020 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.534, B:V.1016, B:L.1017, B:F.1020 Hydrogen bonds: B:R.536, B:S.537, B:R.540, B:R.540, B:Y.541 LMT.15: 9 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541, I.548, F.1020, F.1021 8 PLIP interactions: 8 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:Y.541

1 x HEX: HEXANE(Non-covalent)

HEX.4: 3 residues within 4Å: Chain A: F.458, F.459, R.468 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.458, A:F.458

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: S.84, G.581, T.724, Q.726 Chain C: Q.218, N.231, A.232, S.233 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:Q.218, A:T.724, A:Q.726 Water bridges: A:S.84, A:S.84 GOL.14: 5 residues within 4Å: Chain B: N.189, R.263, D.264, K.267, E.776 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.189, B:E.776 GOL.17: 6 residues within 4Å: Chain A: G.51, G.755, M.774 Chain C: Q.218, G.221, T.222 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.221, A:G.51 GOL.19: 5 residues within 4Å: Chain D: N.122, D.143, F.145, K.147, I.152 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.122

1 x ETE: 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-covalent)

ETE.7: 1 residues within 4Å: Chain A: G.957 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.8: 15 residues within 4Å: Chain A: M.573, M.575, Q.577, F.617, A.618, F.664, F.666, L.668, R.717, P.718, N.719, G.720, L.721, R.815, L.828 16 PLIP interactions: 16 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:L.668, A:L.721, A:L.828 Hydrogen bonds: A:Q.577, A:R.717, A:R.717, A:N.719, A:N.719, A:N.719 Salt bridges: A:R.717

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

EDO.9: 4 residues within 4Å: Chain A: Y.811 Chain E: E.20, R.23, D.44 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:D.44, A:Y.811

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

DDR.11: 11 residues within 4Å: Chain B: V.452, P.455, M.456, Y.467, Y.877, S.880, L.881, V.905, Q.928, L.932, I.935 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.877, B:L.881, B:V.905, B:L.932, B:L.932, B:I.935 Hydrogen bonds: B:Y.467, B:Y.877

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

DDQ.12: 8 residues within 4Å: Chain A: R.8, F.11 Chain B: G.440, V.443, G.444, C.887, A.890, L.891 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

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

OCT.13: 4 residues within 4Å: Chain B: I.27, L.300, D.301, I.337 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.27, B:L.300

1 x D10: DECANE(Non-covalent)

D10.16: 3 residues within 4Å: Chain B: L.25 Chain C: P.455, F.458 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.458

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

CL.18: 2 residues within 4Å: Chain C: G.691, H.692 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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