SMTL ID : 6q4n.1

Fusidic acid bound AcrB_V340A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-2-mer

Ligands

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.1: 4 residues within 4Å: Chain A: G.957, G.959, R.1031, K.1036 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.1031, A:K.1036

3 x FUA: FUSIDIC ACID(Non-covalent)

FUA.2: 8 residues within 4Å: Chain A: G.24, I.27, K.334, I.337, H.338, V.341, V.345 Ligands: LMT.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.27, A:I.337, A:H.338, A:V.345 Salt bridges: A:H.338, A:H.338 FUA.8: 8 residues within 4Å: Chain B: I.27, L.300, K.334, I.337, H.338, V.341, L.377 Ligands: LMT.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.27, B:L.300, B:K.334, B:I.337, B:L.377 Salt bridges: B:H.338 FUA.25: 5 residues within 4Å: Chain C: I.27, L.28, K.334, H.338, V.341 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.27, C:L.28, C:K.334 Salt bridges: C:H.338, C:H.338

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

LMT.3: 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.19 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.11, C:I.15, C:I.19 Hydrogen bonds: C:R.8 LMT.4: 9 residues within 4Å: Chain A: I.27, L.28, V.32, V.341, L.344, F.380, I.390, M.395 Ligands: FUA.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.27, A:I.27, A:V.341, A:L.344, A:F.380, A:F.380, A:I.390 Hydrogen bonds: A:L.28 LMT.5: 8 residues within 4Å: Chain A: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, F.1020 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.1020, A:F.1020 Hydrogen bonds: A:R.536, A:R.536, A:S.537, A:S.537, A:R.540, 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, F.1020 Ligands: D10.19 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.1016, B:F.1020 Hydrogen bonds: B:R.536, B:S.537, B:S.537, B:R.540, B:R.540, B:Y.541 LMT.10: 14 residues within 4Å: Chain B: I.27, L.28, V.32, N.298, L.300, D.301, K.334, I.337, V.341, I.348, P.373, F.380, I.390 Ligands: FUA.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.27, B:I.337, B:V.341, B:I.348, B:P.373, B:F.380, B:F.380, B:I.390 Hydrogen bonds: B:N.298, B:D.301, B:D.301, B:K.334, B:K.334 LMT.11: 9 residues within 4Å: Chain A: R.8, I.18 Chain B: G.436, G.440, V.443, G.444, M.447, C.887, K.955 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.443, A:I.18 Hydrogen bonds: B:G.436 LMT.26: 9 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541, I.548, F.1020 Ligands: OCT.32 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.548, C:F.1020, C:F.1020 Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:R.540, C:Y.541 LMT.27: 10 residues within 4Å: Chain C: R.558, G.911, L.914, A.915, T.917, F.918, R.919, G.920, G.1009, T.1013 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.914, C:F.918, C:T.1013 Hydrogen bonds: C:R.558

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: G.51, W.754, G.755, M.774 Chain C: Q.218, G.221, T.222 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.222, A:G.51 Water bridges: C:Q.218, C:T.222 GOL.7: 7 residues within 4Å: Chain A: R.168, E.309 Chain B: L.75, M.76, Y.77, M.78, N.820 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.168, A:E.309, B:M.78 Water bridges: A:A.165, A:T.169, B:M.76 GOL.13: 6 residues within 4Å: Chain B: L.111, Q.112, M.115, G.126, V.127 Chain C: Q.112 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:V.127, C:Q.112 GOL.31: 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.39: 4 residues within 4Å: Chain A: Y.811 Chain E: E.20, R.23, D.44 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.23, E:R.23, E:D.44, A:Y.811 GOL.40: 5 residues within 4Å: Chain A: T.696, N.700 Chain E: R.23, W.57, H.59 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:R.23, E:H.59, A:N.700, A:D.723

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.12: 12 residues within 4Å: Chain B: M.1, L.30, P.31, A.381, A.384, A.385, G.387, F.388, L.480 Ligands: DDQ.20, D12.24, PTY.28 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.384, B:L.480 Hydrogen bonds: B:G.387 PTY.28: 11 residues within 4Å: Chain B: K.29 Chain C: A.451, V.454, P.455, F.458, F.459, G.460, S.875, C.887 Ligands: PTY.12, PTY.30 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.451, C:V.454, C:F.458, C:F.458, C:F.458 Hydrogen bonds: C:S.875 Salt bridges: B:K.29, B:K.29, B:K.29 PTY.29: 8 residues within 4Å: Chain B: W.13, I.17, L.21 Chain C: S.894, W.895, S.896, K.950, R.1030 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:W.13, B:I.17, B:L.21, C:W.895, C:W.895, C:W.895 Hydrogen bonds: C:S.894, C:W.895, C:S.896, C:R.1030 PTY.30: 13 residues within 4Å: Chain B: R.8, F.11 Chain C: Q.439, G.440, M.447, C.887, A.890, L.891, Y.892, E.893, E.947, D.951 Ligands: PTY.28 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.890, B:F.11 Salt bridges: B:R.8

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

OCT.14: 2 residues within 4Å: Chain B: R.468 Ligands: D10.16 No protein-ligand interaction detected (PLIP) OCT.15: 1 residues within 4Å: Chain B: H.526 No protein-ligand interaction detected (PLIP) OCT.32: 3 residues within 4Å: Chain C: S.523, S.530 Ligands: LMT.26 No protein-ligand interaction detected (PLIP) OCT.33: 2 residues within 4Å: Chain A: W.895 Chain C: W.13 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.13 OCT.34: 1 residues within 4Å: Chain C: A.26 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.26

5 x D10: DECANE(Non-covalent)

D10.16: 6 residues within 4Å: Chain B: F.386, A.457, R.468, V.475, S.476 Ligands: OCT.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.386, B:V.475 D10.17: 4 residues within 4Å: Chain B: V.443, M.447, S.450, A.479 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.479 D10.18: 2 residues within 4Å: Chain B: I.882, W.895 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.882, B:W.895, B:W.895, B:W.895 D10.19: 3 residues within 4Å: Chain B: Y.527, S.530 Ligands: LMT.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.527 D10.35: 7 residues within 4Å: Chain C: M.552, F.556, Y.877, V.909, L.931, I.935 Ligands: HEX.37 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.556, C:F.556, C:F.556, C:Y.877, C:Y.877, C:V.909, C:L.931, C:I.935

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

DDQ.20: 5 residues within 4Å: Chain B: M.1, F.4, F.5, I.15 Ligands: PTY.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.4, B:F.5, B:I.15 DDQ.36: 4 residues within 4Å: Chain C: F.388, R.468, S.471, I.472 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.388, C:I.472

2 x HEX: HEXANE(Non-covalent)

HEX.21: 2 residues within 4Å: Chain B: V.454, F.458 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.454, B:F.458 HEX.37: 3 residues within 4Å: Chain C: F.556, P.874 Ligands: D10.35 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.556

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

SO4.22: 5 residues within 4Å: Chain B: R.239, N.760, D.761 Chain C: P.119, Q.120 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Q.120, C:Q.120, B:D.761, B:D.761 Salt bridges: B:R.239 SO4.38: 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 DDR: (2S)-3-hydroxypropane-1,2-diyl didecanoate(Non-covalent)

DDR.23: 12 residues within 4Å: Chain B: V.452, P.455, M.456, F.459, M.552, Y.877, S.880, L.881, V.905, Q.928, L.932, I.935 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.877, B:L.881, B:V.905, B:Q.928, B:L.932, B:L.932

1 x D12: DODECANE(Non-covalent)

D12.24: 3 residues within 4Å: Chain B: A.385, F.386 Ligands: PTY.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.385

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.
Show / Hide

Multidrug efflux pump subunit AcrB

DARPin

Related Entries With Identical Sequence