SMTL ID : 5nc5.1

Crystal structure of AcrBZ in complex with antibiotic puromycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-3-2-3-mer

Ligands

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

LMT.1: 17 residues within 4Å: Chain A: I.27, L.28, L.30, V.32, I.337, H.338, V.341, L.344, V.345, I.348, P.373, L.376, L.377, F.380, I.390, M.395 Ligands: D10.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.27, A:I.27, A:V.341, A:L.377, A:F.380, A:F.380 Hydrogen bonds: A:L.28, A:L.30 LMT.2: 11 residues within 4Å: Chain A: G.440, G.444, M.447, C.887, A.890, L.891 Chain C: F.4, F.11, V.14, I.15, I.18 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.11, C:I.18 LMT.11: 13 residues within 4Å: Chain A: L.25, K.29 Chain B: S.450, A.451, V.454, P.455, F.458, Q.872, S.875, L.876, I.879, V.883 Ligands: DD9.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.454, B:F.458, B:F.458, B:L.876

8 x D12: DODECANE(Non-covalent)(Non-functional Binders)

D12.3: 10 residues within 4Å: Chain A: P.9, I.10, W.13, I.17, M.20, T.495 Chain B: W.895 Ligands: D10.6, D10.15, DD9.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.9, A:W.13, A:W.13 D12.12: 11 residues within 4Å: Chain A: F.4, R.8, F.11, V.14 Chain B: G.440, V.443, G.444, M.447, C.887, A.890, L.891 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.890, A:F.11 D12.18: 4 residues within 4Å: Ligands: DD9.14, D10.22, DD9.26, D10.27 No protein-ligand interaction detected (PLIP) D12.35: 13 residues within 4Å: Chain B: F.4, R.8, F.11, V.14, I.18 Chain C: M.447, C.887, A.890, L.891, E.893 Ligands: DD9.23, D10.32, D10.48 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.891 D12.39: 7 residues within 4Å: Chain B: I.10 Chain C: F.885, S.894, W.895, S.896, F.1033 Ligands: D10.17 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.895, C:W.895 D12.42: 7 residues within 4Å: Chain A: W.895 Chain C: P.9, I.10, W.13, I.17, M.20 Ligands: D10.4 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.13, C:W.13, C:I.17 D12.43: 10 residues within 4Å: Chain B: L.25 Chain C: V.454, P.455, F.458, F.459, I.879, V.883, C.887 Ligands: DD9.21, D10.40 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.454, C:F.458, C:F.458, C:F.458, C:F.459 D12.44: 6 residues within 4Å: Chain C: F.386, F.388, I.472 Ligands: DD9.37, DD9.45, DD9.46 No protein-ligand interaction detected (PLIP)

26 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.4: 7 residues within 4Å: Chain A: I.882, F.885, L.886, W.895 Chain C: I.17 Ligands: D10.5, D12.42 Ligand excluded by PLIP D10.5: 7 residues within 4Å: Chain A: I.882, F.885, W.895, S.896, F.899, F.1033 Ligands: D10.4 Ligand excluded by PLIP D10.6: 9 residues within 4Å: Chain A: W.13, M.20, L.366, I.370, P.373, L.377, M.496 Ligands: LMT.1, D12.3 Ligand excluded by PLIP D10.8: 8 residues within 4Å: Chain A: V.454, A.457, F.458, F.459, G.460, R.468, I.472 Ligands: DD9.10 Ligand excluded by PLIP D10.9: 4 residues within 4Å: Chain A: A.385, F.386, G.387 Ligands: DD9.14 Ligand excluded by PLIP D10.15: 9 residues within 4Å: Chain A: I.17, L.21 Chain B: I.882, F.885, L.886, W.895 Ligands: D12.3, DD9.16, D10.19 Ligand excluded by PLIP D10.17: 7 residues within 4Å: Chain B: P.9, I.10, W.13, I.17 Chain C: W.895 Ligands: D10.24, D12.39 Ligand excluded by PLIP D10.19: 10 residues within 4Å: Chain B: L.881, I.882, F.885, W.895, S.896, F.899, M.902, F.1033 Ligands: D10.15, DD9.16 Ligand excluded by PLIP D10.22: 8 residues within 4Å: Chain B: V.454, A.457, F.458, R.468, I.472, V.475 Ligands: D12.18, D10.27 Ligand excluded by PLIP D10.24: 6 residues within 4Å: Chain B: W.13, M.20, L.366, I.370, M.496 Ligands: D10.17 Ligand excluded by PLIP D10.25: 11 residues within 4Å: Chain B: M.456, F.459, Y.467, F.556, A.873, Y.877, Q.928, L.931, L.932, I.935 Ligands: D10.30 Ligand excluded by PLIP D10.27: 11 residues within 4Å: Chain B: V.382, F.386, F.388, R.468, I.472, V.475, S.476, A.479 Ligands: D12.18, D10.22, DD9.26 Ligand excluded by PLIP D10.28: 5 residues within 4Å: Chain B: M.1, F.4, F.5 Ligands: DD9.23, D10.36 Ligand excluded by PLIP D10.30: 15 residues within 4Å: Chain B: V.452, P.455, M.456, F.459, L.876, Y.877, S.880, L.881, V.884, M.902, V.905, L.932, I.935, A.939 Ligands: D10.25 Ligand excluded by PLIP D10.31: 13 residues within 4Å: Chain B: I.27, L.28, L.30, V.32, N.298, L.300, I.337, V.340, V.341, F.380, I.390, M.395, M.398 Ligand excluded by PLIP D10.32: 12 residues within 4Å: Chain B: I.15, I.18, I.19, A.22, A.381, V.382, A.385, L.480 Ligands: DD9.20, DD9.23, DD9.33, D12.35 Ligand excluded by PLIP D10.36: 3 residues within 4Å: Ligands: DD9.23, D10.28, D10.47 Ligand excluded by PLIP D10.38: 8 residues within 4Å: Chain C: I.27, V.32, L.300, K.334, I.337, V.341, F.380, I.390 Ligand excluded by PLIP D10.40: 9 residues within 4Å: Chain B: L.25 Chain C: A.457, F.458, F.459, R.468 Ligands: DD9.20, DD9.21, DD9.37, D12.43 Ligand excluded by PLIP D10.47: 3 residues within 4Å: Ligands: DD9.23, D10.36, D10.48 Ligand excluded by PLIP D10.48: 7 residues within 4Å: Chain C: Q.439, V.443, M.447, L.891 Ligands: DD9.23, D12.35, D10.47 Ligand excluded by PLIP D10.49: 1 residues within 4Å: Ligands: D10.50 Ligand excluded by PLIP D10.50: 6 residues within 4Å: Chain C: M.1, F.4, F.5, I.15, I.487 Ligands: D10.49 Ligand excluded by PLIP D10.51: 7 residues within 4Å: Chain C: A.878, L.881, I.882, F.885, M.902 Ligands: D10.52, D10.53 Ligand excluded by PLIP D10.52: 7 residues within 4Å: Chain C: L.881, M.902, L.903, V.905, P.906 Ligands: D10.51, D10.53 Ligand excluded by PLIP D10.53: 7 residues within 4Å: Chain C: F.556, P.874, Y.877, A.878, L.881 Ligands: D10.51, D10.52 Ligand excluded by PLIP

14 x DD9: nonane(Non-functional Binders)(Non-covalent)

DD9.7: 9 residues within 4Å: Chain A: I.19, A.22, L.25, A.26, A.381, V.382, A.384, A.385 Ligands: DD9.13 No protein-ligand interaction detected (PLIP) DD9.10: 5 residues within 4Å: Chain A: F.386, F.388, R.468, I.472 Ligands: D10.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.386 DD9.13: 8 residues within 4Å: Chain A: I.18, L.21, A.22, L.25 Chain B: M.447, V.883 Ligands: DD9.7, LMT.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.18 DD9.14: 3 residues within 4Å: Ligands: D10.9, D12.18, DD9.26 No protein-ligand interaction detected (PLIP) DD9.16: 3 residues within 4Å: Ligands: D12.3, D10.15, D10.19 No protein-ligand interaction detected (PLIP) DD9.20: 6 residues within 4Å: Chain B: A.385 Chain C: F.458 Ligands: D10.32, DD9.33, D10.40, DD9.46 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.458 DD9.21: 8 residues within 4Å: Chain B: I.18, L.21, A.22, L.25 Chain C: I.879, V.883 Ligands: D10.40, D12.43 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.25 DD9.23: 8 residues within 4Å: Chain B: F.4, F.11 Ligands: D10.28, D10.32, D12.35, D10.36, D10.47, D10.48 No protein-ligand interaction detected (PLIP) DD9.26: 5 residues within 4Å: Chain B: F.386 Ligands: DD9.14, D12.18, D10.27, DD9.33 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.386 DD9.29: 7 residues within 4Å: Chain A: L.21, L.25, L.28 Chain B: S.875, A.878, I.879, I.882 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.879, B:I.882, A:L.28 DD9.33: 6 residues within 4Å: Chain B: A.385, F.386 Ligands: DD9.20, DD9.26, D10.32, DD9.46 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.385 DD9.37: 7 residues within 4Å: Chain C: A.457, F.458, R.468 Ligands: D10.40, D12.44, DD9.45, DD9.46 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.458, C:F.458 DD9.45: 4 residues within 4Å: Chain C: F.386 Ligands: DD9.37, D12.44, DD9.46 No protein-ligand interaction detected (PLIP) DD9.46: 6 residues within 4Å: Chain C: F.458 Ligands: DD9.20, DD9.33, DD9.37, D12.44, DD9.45 No protein-ligand interaction detected (PLIP)

1 x PUY: PUROMYCIN(Non-covalent)

PUY.34: 13 residues within 4Å: Chain B: S.134, F.136, V.139, F.178, M.573, F.615, F.617, F.628, F.664, F.666, L.668, P.669, V.672 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.617, B:F.666, B:P.669 Hydrogen bonds: B:V.672 pi-Stacking: B:F.136, B:Y.327

1 x HEX: HEXANE(Non-covalent)

HEX.41: 7 residues within 4Å: Chain C: V.382, F.386, I.472, V.475, S.476, A.479, L.480 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.386

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., An allosteric transport mechanism for the AcrAB-TolC Multidrug Efflux Pump. Elife (2017)

Release Date

2017-04-12

Peptides

Multidrug efflux pump subunit AcrB: ABC
DARPin: DE
Multidrug efflux pump accessory protein AcrZ: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Multidrug efflux pump subunit AcrB

DARPin

Multidrug efflux pump accessory protein AcrZ

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