SMTL ID : 5jmn.1

Fusidic acid bound AcrB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-2-mer

Ligands

3 x FUA: FUSIDIC ACID(Non-covalent)

FUA.1: 6 residues within 4Å: Chain A: I.27, K.334, I.337, H.338, V.341 Ligands: LMT.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.27, A:K.334, A:I.337 Salt bridges: A:H.338, A:H.338 FUA.10: 6 residues within 4Å: Chain B: I.27, L.300, K.334, H.338, V.341 Ligands: LMT.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.27, B:L.300, B:V.341 Salt bridges: B:H.338 FUA.22: 5 residues within 4Å: Chain C: V.32, K.334, H.338, V.341 Ligands: LMT.25 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.32, C:V.341 Salt bridges: C:H.338, C:H.338

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

LMT.2: 9 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 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:M.447, A:A.890, C:F.11, C:I.18, C:I.18 Hydrogen bonds: A:G.440, C:R.8 LMT.3: 8 residues within 4Å: Chain A: I.27, L.28, V.32, V.341, I.348, F.380, I.390 Ligands: FUA.1 8 PLIP interactions: 8 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 Hydrogen bonds: A:L.28 LMT.4: 10 residues within 4Å: Chain A: R.8, F.11, I.18 Chain B: Q.439, G.440, V.443, G.444, A.890, L.891 Ligands: P3G.19 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.443, B:A.890, A:I.18 Hydrogen bonds: B:Q.439, B:A.890, A:R.8 Water bridges: B:G.440 LMT.11: 10 residues within 4Å: Chain B: S.530, G.533, I.534, R.536, S.537, R.540, Y.541, V.1016, F.1020 Ligands: D10.20 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.1016 Hydrogen bonds: B:R.536, B:R.536, B:R.540, B:R.540, B:Y.541 LMT.12: 2 residues within 4Å: Chain B: R.363 Ligands: OCT.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.363 LMT.13: 10 residues within 4Å: Chain B: I.27, N.298, L.300, D.301, A.304, K.334, I.337, V.341, F.380 Ligands: FUA.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.27, B:I.337, B:F.380, B:F.380 Hydrogen bonds: B:N.298, B:D.301, B:D.301 Water bridges: B:I.27, B:L.28 LMT.23: 7 residues within 4Å: Chain C: A.22, L.25, A.26, K.29, A.381, A.384, A.385 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.385 Hydrogen bonds: C:L.25 LMT.24: 6 residues within 4Å: Chain C: S.530, G.533, R.536, S.537, R.540, Y.541 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.536, C:R.536, C:S.537, C:S.537, C:R.540, C:Y.541 LMT.25: 6 residues within 4Å: Chain C: L.28, V.32, V.341, F.380, I.390 Ligands: FUA.22 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.341, C:F.380, C:F.380, C:I.390 LMT.26: 3 residues within 4Å: Chain C: G.511, F.512, W.515 No protein-ligand interaction detected (PLIP)

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

SO4.5: 6 residues within 4Å: Chain A: R.185, E.273, G.755, G.756, Y.772, M.774 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.273 Salt bridges: A:R.185 SO4.27: 2 residues within 4Å: Chain C: G.691, H.692 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.692 Water bridges: C:E.693 Salt bridges: C:K.55

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: T.696, N.700 Chain E: R.23, W.57 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:H.59, A:N.700 Water bridges: E:R.23, A:N.700 GOL.14: 7 residues within 4Å: Chain B: Q.124, R.239, Y.758, N.760, D.761 Chain C: P.119, Q.120 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:Q.120, B:Q.124, B:R.239, B:R.239, B:Y.758, B:D.761 GOL.15: 8 residues within 4Å: Chain B: Q.108, L.111, Q.112, M.115, G.126, V.127 Chain C: Q.112, P.116 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.108, B:Q.112, B:V.127, B:V.127, C:Q.112 Water bridges: B:V.129 GOL.28: 8 residues within 4Å: Chain C: R.185, E.273, N.274, G.755, G.756, S.757, Y.772, M.774 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.185, C:R.185, C:G.756 GOL.29: 7 residues within 4Å: Chain A: G.689 Chain C: A.160, N.161, D.764, R.765, R.767, K.769 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.161, C:K.769, C:K.769 Water bridges: C:D.156, C:R.765, C:R.767, A:G.689 GOL.39: 3 residues within 4Å: Chain D: D.143, K.147, I.152 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.806, B:S.806 GOL.40: 5 residues within 4Å: Chain E: I.114, H.118, D.143, K.147, I.152 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.732 GOL.41: 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:D.44, A:Y.811

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

ETE.7: 2 residues within 4Å: Chain A: A.384, A.385 No protein-ligand interaction detected (PLIP) ETE.8: 4 residues within 4Å: Chain A: G.957, G.959, I.961, R.1031 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.960 ETE.36: 4 residues within 4Å: Chain C: E.640, T.917, R.919, G.920 No protein-ligand interaction detected (PLIP)

2 x HEX: HEXANE(Non-covalent)

HEX.9: 3 residues within 4Å: Chain A: W.13, I.17 Ligands: PTY.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.13, A:W.13, A:I.17 HEX.38: 4 residues within 4Å: Chain C: M.1, L.483, L.486 Ligands: PTY.31 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.483, C:L.486

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.16: 6 residues within 4Å: Chain B: I.882, F.885, W.895, F.899, F.1033 Ligands: HEX.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.882, B:F.885, B:W.895, B:W.895, B:F.899, B:F.1033 Hydrogen bonds: B:S.896 PTY.30: 7 residues within 4Å: Chain B: K.29 Chain C: V.454, F.458, Q.872, S.875, V.883 Ligands: PTY.31 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.454, C:V.454, C:F.458, C:F.458, C:V.883 Hydrogen bonds: C:S.875 PTY.31: 12 residues within 4Å: Chain B: R.8, F.11, I.18 Chain C: Q.439, M.447, A.890, L.891, Y.892, E.893, E.947 Ligands: PTY.30, HEX.38 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.890, C:L.891, B:F.11 Hydrogen bonds: C:Q.439 Salt bridges: B:R.8 PTY.32: 10 residues within 4Å: Chain B: W.13, L.21 Chain C: I.882, F.885, L.886, S.894, W.895, S.896, R.1030 Ligands: OCT.18 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.882, C:F.885, C:L.886, C:W.895, B:W.13 Hydrogen bonds: C:W.895, C:S.896, C:R.1030 Salt bridges: C:R.1030

4 x D12: DODECANE(Non-covalent)

D12.17: 5 residues within 4Å: Chain B: M.1, V.443, M.447, S.450, A.479 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.443 D12.33: 4 residues within 4Å: Chain C: M.552, F.556, V.557, I.935 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.556, C:I.935 D12.34: 3 residues within 4Å: Chain C: G.387, F.388, R.468 No protein-ligand interaction detected (PLIP) D12.35: 3 residues within 4Å: Chain A: W.895 Chain C: P.9, W.13 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.9

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

OCT.18: 3 residues within 4Å: Chain B: T.495 Ligands: LMT.12, PTY.32 No protein-ligand interaction detected (PLIP) OCT.37: 1 residues within 4Å: Chain C: M.1 No protein-ligand interaction detected (PLIP)

1 x P3G: 3,6,9,12,15-PENTAOXAHEPTADECANE(Non-covalent)

P3G.19: 3 residues within 4Å: Chain A: N.3 Chain B: Q.439 Ligands: LMT.4 No protein-ligand interaction detected (PLIP)

2 x D10: DECANE(Non-covalent)

D10.20: 2 residues within 4Å: Chain B: S.530 Ligands: LMT.11 No protein-ligand interaction detected (PLIP) D10.21: 3 residues within 4Å: Chain A: K.29 Chain B: A.451, V.454 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.454

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oswald, C. et al., Transport of lipophilic carboxylates is mediated by transmembrane helix 2 in multidrug transporter AcrB. Nat Commun (2016)

Release Date

2016-12-21

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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