SMTL ID : 6zof.1

Fusidic acid binding to the TM7/TM8 groove of AcrB-F380A T protomer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-3-2-mer

Ligands

5 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: F.4, R.8, F.11, I.18 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:A.890, C:F.11, C:I.18, C:I.18 Hydrogen bonds: C:R.8, C:R.8 Salt bridges: C:R.8 LMT.2: 7 residues within 4Å: Chain A: S.530, G.533, R.536, Y.541, L.544, L.1017, F.1020 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.544, A:L.1017, A:F.1020, A:F.1020, A:F.1020 Hydrogen bonds: A:R.536, A:Y.541 LMT.9: 9 residues within 4Å: Chain B: S.530, G.533, R.536, S.537, R.540, Y.541, V.1016, L.1017, F.1020 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.1016, B:L.1017, B:F.1020 Hydrogen bonds: B:S.530, B:R.536, B:S.537, B:R.540, B:Y.541 LMT.10: 14 residues within 4Å: Chain B: I.27, L.30, V.32, N.298, L.300, D.301, A.304, K.334, I.337, V.341, L.383, S.389, I.390, T.394 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.30, B:I.337, B:V.341, B:L.383 Hydrogen bonds: B:I.27, B:N.298, B:D.301, B:K.334, B:K.334 LMT.12: 8 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, 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:R.540, C:Y.541

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

SO4.3: 4 residues within 4Å: Chain A: K.55, G.691, H.692 Chain C: G.766 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.692 Salt bridges: A:K.55 SO4.13: 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

1 x D10: DECANE(Non-covalent)

D10.4: 2 residues within 4Å: Chain B: K.29, A.384 No protein-ligand interaction detected (PLIP)

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

DDQ.5: 3 residues within 4Å: Chain A: F.11 Chain B: G.440, C.887 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.11

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain B: R.239, Y.758, N.760, D.761 Chain C: P.119, Q.120, E.121 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.758, B:D.761, B:D.761, C:Q.120, C:E.121

1 x FUA: FUSIDIC ACID(Non-covalent)

FUA.7: 12 residues within 4Å: Chain B: Y.545, V.549, Y.877, S.880, L.881, V.884, V.901, M.902, L.903, V.905, P.906, I.935 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.549, B:L.881, B:V.884, B:V.901, B:L.903, B:I.935 Hydrogen bonds: B:Y.545, B:S.880, B:S.880

1 x R16: HEXADECANE(Non-covalent)

R16.8: 3 residues within 4Å: Chain B: K.29 Chain C: F.458, S.875 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.11: 12 residues within 4Å: Chain B: I.10, W.13 Chain C: I.882, F.885, E.893, S.894, W.895, S.896, R.1030, F.1033, S.1034, R.1035 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.882, C:F.885, C:W.895, C:W.895, C:W.895, C:W.895, B:W.13 Hydrogen bonds: C:E.893, C:W.895, C:S.896 Salt bridges: C:K.950, C:R.1030, C:R.1035

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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