SMTL ID : 6q4p.1

Fusidic acid bound AcrB_N298A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-2-mer

Ligands

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

LMT.1: 8 residues within 4Å: Chain A: I.27, L.28, V.32, V.341, I.348, F.380, I.390 Ligands: LMT.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.27, A:I.27, A:V.341, A:I.348, A:F.380, A:F.380, A:I.390 LMT.2: 12 residues within 4Å: Chain A: G.440, G.444, M.447, C.887, A.890, L.891, E.893 Chain C: F.4, R.8, F.11, I.18 Ligands: DDQ.34 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.11, C:I.18, C:I.18, A:M.447 Hydrogen bonds: C:R.8, A:G.440, A:E.893 Salt bridges: C:R.8 LMT.3: 11 residues within 4Å: Chain A: L.25, L.28 Chain B: S.450, V.454, F.458, N.871, Q.872, S.875, L.876, I.879 Ligands: LMT.1 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.458, B:F.458, B:L.876, B:I.879 Hydrogen bonds: B:F.458, B:N.871, B:Q.872, B:S.875 Salt bridges: A:K.29 LMT.4: 9 residues within 4Å: Chain A: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, L.1017, F.1020 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.1017, A:F.1020 Hydrogen bonds: A:R.536, A:R.536, A:S.537, A:Y.541 LMT.11: 8 residues within 4Å: Chain B: S.530, G.533, R.536, S.537, R.540, Y.541, F.1020 Ligands: OCT.21 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.536, B:R.536, B:S.537, B:S.537, B:R.540, B:Y.541 LMT.12: 10 residues within 4Å: Chain B: I.27, L.28, L.30, V.32, A.298, D.301, I.337, V.341, F.380, I.390 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.27, B:I.337, B:V.341, B:F.380, B:F.380, B:I.390 Hydrogen bonds: B:L.28 LMT.13: 6 residues within 4Å: Chain B: I.19, K.29, G.296, V.382, A.384, L.480 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.19, B:V.382, B:L.480 LMT.27: 9 residues within 4Å: Chain C: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, F.1020 Ligands: D12.31 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.1020 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:R.540, C:Y.541 LMT.28: 6 residues within 4Å: Chain B: K.29 Chain C: F.458, L.868, N.871, Q.872, S.875 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.458, C:F.458, C:F.458 Hydrogen bonds: C:S.875 Salt bridges: B:K.29 LMT.29: 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

3 x D12: DODECANE(Non-covalent)

D12.5: 4 residues within 4Å: Chain A: A.457, F.458, R.468, I.472 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.458 D12.16: 2 residues within 4Å: Chain B: W.895 Ligands: D10.26 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.895 D12.31: 3 residues within 4Å: Chain C: S.523, S.530 Ligands: LMT.27 No protein-ligand interaction detected (PLIP)

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

DDQ.6: 4 residues within 4Å: Chain A: P.9, W.13, I.17 Chain B: W.895 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.13, A:I.17 DDQ.18: 5 residues within 4Å: Chain A: F.4, F.11 Chain B: G.440, G.444, C.887 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.11 DDQ.19: 4 residues within 4Å: Chain B: F.458, F.459, R.468, I.472 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.458, B:F.458, B:I.472 DDQ.33: 5 residues within 4Å: Chain C: F.388, A.457, R.468, S.471 Ligands: DDQ.35 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.388, C:A.457 DDQ.34: 3 residues within 4Å: Chain C: F.4, F.5 Ligands: LMT.2 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.5 DDQ.35: 4 residues within 4Å: Chain C: A.457, F.458, R.468 Ligands: DDQ.33 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: K.55, G.691, H.692, E.693 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.55, A:H.692, A:E.693 Water bridges: A:Q.58 GOL.8: 5 residues within 4Å: Chain A: A.47, S.48, Q.125, G.126, S.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.125, A:S.128, A:S.128 Water bridges: A:S.46, A:S.48 GOL.9: 7 residues within 4Å: Chain A: G.51, D.276, G.755, M.774 Chain C: Q.218, G.221, T.222 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.51, A:D.276 Water bridges: A:D.276, A:R.780, C:Q.218, C:T.222 GOL.25: 7 residues within 4Å: Chain A: R.168, E.309 Chain B: L.75, M.76, Y.77, M.78, N.820 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.168, A:E.309, B:L.75, B:M.78 GOL.41: 7 residues within 4Å: Chain C: R.185, E.273, N.274, G.755, G.756, Y.772, M.774 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.185, C:R.185, C:G.756 GOL.44: 4 residues within 4Å: Chain A: Y.811 Chain E: E.20, R.23, D.44 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.23, E:R.23, A:Y.811

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

HEX.10: 2 residues within 4Å: Chain A: S.523, Y.527 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.527 HEX.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x FUA: FUSIDIC ACID(Non-covalent)

FUA.14: 6 residues within 4Å: Chain B: G.24, I.27, L.300, K.334, H.338, V.341 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.27, B:I.27, B:L.300 Salt bridges: B:H.338

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.15: 10 residues within 4Å: Chain B: F.4, R.8, F.11 Chain C: Q.439, V.443, M.447, A.890, L.891, Y.892, E.947 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:V.443, C:A.890, B:F.4, B:F.11, B:F.11 Hydrogen bonds: C:Q.439 Salt bridges: B:R.8 PTY.30: 11 residues within 4Å: Chain B: W.13 Chain C: A.878, I.882, F.885, S.894, W.895, S.896, K.950, R.1030, F.1033, S.1034 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain C Hydrophobic interactions: B:W.13, B:W.13, C:A.878, C:I.882, C:I.882, C:F.885, C:W.895, C:W.895 Hydrogen bonds: C:W.895, C:S.896, C:S.896, C:K.950, C:K.950 Salt bridges: C:K.950, C:R.1030

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

DDR.17: 15 residues within 4Å: Chain B: V.452, M.456, F.459, Y.467, M.552, F.556, Y.877, S.880, L.881, V.884, V.905, Q.928, L.931, L.932, I.935 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.556, B:Y.877, B:L.881, B:V.884, B:V.905, B:V.905, B:L.931, B:L.932, B:I.935, B:I.935 Hydrogen bonds: B:Y.467, B:Y.877

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

OCT.20: 1 residues within 4Å: Chain B: F.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.4 OCT.21: 3 residues within 4Å: Chain B: Y.527, S.530 Ligands: LMT.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.527 OCT.36: 2 residues within 4Å: Chain C: M.552, F.556 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.556, C:F.556

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

CL.22: 2 residues within 4Å: Chain B: N.361, F.362 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain C: G.691, H.692 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain C: Q.228, Q.229, L.230 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain C: N.231, S.233 Ligand excluded by PLIP CL.40: 5 residues within 4Å: Chain C: M.575, F.617, R.717, N.719, L.828 Ligand excluded by PLIP

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

SO4.23: 5 residues within 4Å: Chain B: R.239, N.760, D.761 Chain C: P.119, Q.120 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.761, C:Q.120, C:Q.120 Salt bridges: B:R.239 SO4.24: 3 residues within 4Å: Chain B: K.55, G.691, H.692 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.692 Water bridges: B:Q.58, B:Q.58, B:L.690, B:G.691, B:E.693 Salt bridges: B:K.55

1 x D10: DECANE(Non-covalent)

D10.26: 7 residues within 4Å: Chain B: F.885, W.895, S.896, F.899, F.1033, S.1034 Ligands: D12.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.885, B:F.899, B:F.1033

1 x C14: TETRADECANE(Non-covalent)

C14.32: 2 residues within 4Å: Chain C: W.13, T.495 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.13, C:W.13

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

ETE.42: 3 residues within 4Å: Chain C: T.917, F.918, R.919 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.558

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tam, H.K. et al., Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB. J.Mol.Biol. (2020)

Release Date

2019-11-13

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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