SMTL ID : 6baj.1

Cryo-EM structure of lipid bilayer in the native cell membrane nanoparticles of AcrB

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

31 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)(Non-functional Binders)

PTY.1: 11 residues within 4Å: Chain A: F.4, R.8, F.11, V.14, I.15, I.18 Chain B: A.890, L.891 Ligands: PTY.2, D12.29, D12.31 Ligand excluded by PLIP PTY.2: 6 residues within 4Å: Chain A: M.1, F.4, F.5 Ligands: PTY.1, PTY.3, PTY.4 Ligand excluded by PLIP PTY.3: 9 residues within 4Å: Chain A: M.1, Q.439 Ligands: PTY.2, PTY.4, PTY.7, PTY.8, PTY.34, PTY.35, PTY.42 Ligand excluded by PLIP PTY.4: 6 residues within 4Å: Ligands: PTY.2, PTY.3, D12.27, PTY.34, PTY.40, PTY.42 Ligand excluded by PLIP PTY.5: 6 residues within 4Å: Chain A: F.458 Ligands: PTY.6, PTY.7, PTY.8, PTY.37, PTY.39 Ligand excluded by PLIP PTY.6: 10 residues within 4Å: Chain A: A.26, K.29, A.384, A.385, F.386 Ligands: PTY.5, PTY.7, PTY.8, PTY.17, PTY.23 Ligand excluded by PLIP PTY.7: 18 residues within 4Å: Chain A: I.19, V.382, F.386, V.443, A.446, M.447, S.450, V.454, F.458, R.468, I.472, V.475, L.480, V.482, L.483 Ligands: PTY.3, PTY.5, PTY.6 Ligand excluded by PLIP PTY.8: 6 residues within 4Å: Ligands: PTY.3, PTY.5, PTY.6, PTY.23, PTY.39, PTY.42 Ligand excluded by PLIP PTY.9: 5 residues within 4Å: Chain A: K.334, H.338, V.341, K.342 Ligands: D12.11 Ligand excluded by PLIP PTY.16: 8 residues within 4Å: Chain B: M.1, F.4, F.5 Ligands: PTY.25, D12.27, D12.28, D12.29, PTY.33 Ligand excluded by PLIP PTY.17: 12 residues within 4Å: Chain A: L.21, A.22, K.29 Chain B: V.454, P.455, F.458, F.459, G.460, I.879, V.883 Ligands: PTY.6, PTY.23 Ligand excluded by PLIP PTY.18: 6 residues within 4Å: Chain B: L.886, S.894, W.895, S.896, F.1033 Ligands: D12.10 Ligand excluded by PLIP PTY.19: 7 residues within 4Å: Chain B: I.27, K.334, I.337, V.341, L.344, F.380 Ligands: PTY.22 Ligand excluded by PLIP PTY.20: 7 residues within 4Å: Chain B: I.10, W.13, I.17, M.20 Chain C: W.895 Ligands: PTY.22, PTY.38 Ligand excluded by PLIP PTY.21: 9 residues within 4Å: Chain B: F.556, V.557, P.874, Y.877, A.878, L.881, M.902, V.905, V.909 Ligand excluded by PLIP PTY.22: 9 residues within 4Å: Chain B: W.13, M.20, L.366, T.369, P.373, L.376, L.377 Ligands: PTY.19, PTY.20 Ligand excluded by PLIP PTY.23: 9 residues within 4Å: Chain B: F.386, V.454, F.458, V.475 Ligands: PTY.6, PTY.8, PTY.17, PTY.26, D12.28 Ligand excluded by PLIP PTY.24: 12 residues within 4Å: Chain B: L.25, A.26, K.29, A.381, A.384 Chain C: A.451, V.454, F.458, V.883 Ligands: PTY.25, PTY.40, PTY.41 Ligand excluded by PLIP PTY.25: 13 residues within 4Å: Chain B: R.8, F.11, I.15, I.18, I.19 Chain C: G.440, M.447, C.887, L.891, E.947 Ligands: PTY.16, PTY.24, PTY.33 Ligand excluded by PLIP PTY.26: 6 residues within 4Å: Chain B: A.457, I.472, V.475, A.479, L.480 Ligands: PTY.23 Ligand excluded by PLIP PTY.32: 12 residues within 4Å: Chain A: S.875, I.879, W.895 Chain C: P.9, I.10, W.13, I.17, M.20, L.21, G.24, L.28 Ligands: D12.15 Ligand excluded by PLIP PTY.33: 5 residues within 4Å: Chain C: V.443 Ligands: PTY.16, PTY.25, D12.27, PTY.40 Ligand excluded by PLIP PTY.34: 12 residues within 4Å: Chain C: M.1, F.4, F.5, F.11, I.19, L.483 Ligands: PTY.3, PTY.4, PTY.35, PTY.39, PTY.40, PTY.41 Ligand excluded by PLIP PTY.35: 12 residues within 4Å: Chain A: G.440, V.443, M.447, A.890 Chain C: F.4, R.8, F.11, I.18, I.19 Ligands: PTY.3, PTY.34, PTY.39 Ligand excluded by PLIP PTY.36: 9 residues within 4Å: Chain C: I.27, K.334, I.337, H.338, V.341, P.373, F.380, I.390, M.395 Ligand excluded by PLIP PTY.37: 12 residues within 4Å: Chain A: A.451, V.454, P.455, F.458, I.879, V.883, C.887 Chain C: L.25, A.26, K.29 Ligands: PTY.5, PTY.39 Ligand excluded by PLIP PTY.38: 5 residues within 4Å: Chain B: I.17 Chain C: I.879, W.895, F.1033 Ligands: PTY.20 Ligand excluded by PLIP PTY.39: 10 residues within 4Å: Chain C: I.19, A.385, F.386, L.480 Ligands: PTY.5, PTY.8, PTY.34, PTY.35, PTY.37, PTY.42 Ligand excluded by PLIP PTY.40: 12 residues within 4Å: Chain C: M.1, Q.439, S.450, V.475, A.479, V.482, L.486 Ligands: PTY.4, PTY.24, PTY.33, PTY.34, PTY.42 Ligand excluded by PLIP PTY.41: 11 residues within 4Å: Chain C: V.454, A.457, F.458, R.468, I.472, V.475, S.476, A.479 Ligands: PTY.24, PTY.34, PTY.42 Ligand excluded by PLIP PTY.42: 6 residues within 4Å: Ligands: PTY.3, PTY.4, PTY.8, PTY.39, PTY.40, PTY.41 Ligand excluded by PLIP

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

D12.10: 6 residues within 4Å: Chain A: I.10, W.13 Chain B: W.895 Ligands: D12.12, D12.14, PTY.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.10, A:W.13 D12.11: 7 residues within 4Å: Chain A: I.27, V.341, I.348, P.373, L.376, F.380 Ligands: PTY.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.27, A:V.341, A:I.348, A:P.373, A:L.376, A:F.380, A:F.380 D12.12: 4 residues within 4Å: Chain A: M.20, L.21, G.24 Ligands: D12.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.21 D12.13: 4 residues within 4Å: Chain A: S.523, H.526, Y.527, L.976 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.527, A:L.976 D12.14: 4 residues within 4Å: Chain A: W.13, I.370, M.496 Ligands: D12.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.13, A:I.370 D12.15: 3 residues within 4Å: Chain A: I.882, F.899 Ligands: PTY.32 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.882, A:F.899 D12.27: 3 residues within 4Å: Ligands: PTY.4, PTY.16, PTY.33 No protein-ligand interaction detected (PLIP) D12.28: 8 residues within 4Å: Chain B: P.2, Q.439, V.482, L.483 Ligands: PTY.16, PTY.23, D12.29, D12.31 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.2, B:V.482 D12.29: 4 residues within 4Å: Ligands: PTY.1, PTY.16, D12.28, D12.31 No protein-ligand interaction detected (PLIP) D12.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D12.31: 3 residues within 4Å: Ligands: PTY.1, D12.28, D12.29 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiu, W. et al., Structure and activity of lipid bilayer within a membrane-protein transporter. Proc.Natl.Acad.Sci.USA (2018)

Release Date

2018-12-19

Peptides

Multidrug efflux pump subunit AcrB: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

Membrane

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

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