SMTL ID : 7rr8.1

Multidrug efflux pump subunit AcrB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

13 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 17 residues within 4Å: Chain A: G.440, G.444, M.447, C.887, A.890, L.891, E.893 Chain B: F.4, R.8, F.11, I.18, I.19, A.22 Ligands: PTY.2, PTY.3, D12.4, PTY.10 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.11, B:I.18, B:A.22, A:M.447 Salt bridges: B:R.8 Hydrogen bonds: A:E.893 PTY.2: 4 residues within 4Å: Chain A: Q.439 Chain B: F.4 Ligands: PTY.1, PTY.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.439 PTY.3: 12 residues within 4Å: Chain A: F.458, R.468 Chain B: A.22, A.26, K.29, V.382, A.384, A.385, F.386 Ligands: PTY.1, D12.4, D12.7 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.22, B:A.26, B:V.382, B:F.386 Salt bridges: B:K.29, A:R.468 Hydrogen bonds: A:R.468 PTY.8: 14 residues within 4Å: Chain A: F.5, R.8, F.11, I.15, I.18 Chain C: G.440, V.443, G.444, M.447, C.887, A.890, L.891, E.893 Ligands: PTY.19 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:F.5, A:F.5, A:F.11, A:I.15, A:I.15, A:I.18, A:I.18, C:V.443, C:M.447, C:A.890, C:L.891 Salt bridges: A:R.8 Hydrogen bonds: C:G.444, C:E.893, C:E.893 PTY.9: 10 residues within 4Å: Chain A: L.25, K.29 Chain C: A.451, V.454, P.455, F.458, V.475, I.879, V.883 Ligands: PTY.21 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.454, C:P.455, C:P.455, C:F.458, C:F.458, C:F.458, C:F.458, C:V.475, C:I.879, C:V.883, C:V.883 Salt bridges: A:K.29, A:K.29 PTY.10: 12 residues within 4Å: Chain B: M.1, F.4, F.5, I.19, L.480, L.483, I.487 Ligands: PTY.1, PTY.2, PTY.11, D12.16, D12.17 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.1, B:I.19, B:L.480, B:L.483, B:I.487 PTY.11: 7 residues within 4Å: Chain B: Q.439, V.443, L.891 Ligands: PTY.10, D12.16, D12.17, PTY.18 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.443, B:V.443, B:L.891 Hydrogen bonds: B:Q.439 PTY.12: 12 residues within 4Å: Chain B: F.386, F.388, S.450, V.454, A.457, F.458, R.468, S.471, I.472, V.475, A.479 Ligands: D12.15 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.454, B:A.457, B:F.458, B:I.472, B:V.475, B:V.475, B:V.475, B:A.479 Salt bridges: B:R.468 PTY.13: 14 residues within 4Å: Chain B: V.454, P.455, F.458, F.459, S.875, I.879, V.883 Chain C: I.18, L.21, A.22, L.25 Ligands: D12.14, D12.15, D12.24 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:P.455, B:I.879, B:V.883, B:V.883, C:I.18, C:L.21, C:A.22, C:L.25 Hydrogen bonds: B:F.459, B:F.459 PTY.18: 11 residues within 4Å: Chain B: C.887, A.890, L.891 Chain C: F.4, R.8, F.11, V.14 Ligands: PTY.11, PTY.20, D12.25, D12.26 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.4, C:F.11, C:F.11, C:V.14, B:A.890, B:L.891 Hydrogen bonds: C:R.8 Salt bridges: C:R.8 PTY.19: 8 residues within 4Å: Chain C: M.1, N.3, Q.439, V.443, L.486 Ligands: PTY.8, PTY.20, D12.26 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:M.1, C:V.443, C:L.486 Hydrogen bonds: C:Q.439 PTY.20: 10 residues within 4Å: Chain C: M.1, N.3, F.4, F.5, I.15, I.487 Ligands: PTY.18, PTY.19, D12.25, D12.26 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.4, C:F.4, C:F.4, C:F.5, C:I.15, C:I.15 Hydrogen bonds: C:M.1, C:N.3 PTY.21: 12 residues within 4Å: Chain C: V.382, F.386, F.458, R.468, I.472, V.475, S.476, A.479, L.480, L.483 Ligands: PTY.9, D12.22 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.382, C:F.386, C:F.386, C:I.472, C:V.475, C:A.479, C:L.480, C:L.483 Salt bridges: C:R.468

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

D12.4: 9 residues within 4Å: Chain A: M.447, A.451, F.458, V.883, C.887 Chain B: I.18, L.25 Ligands: PTY.1, PTY.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.451, A:F.458, A:V.883, A:V.883, B:I.18, B:L.25 D12.5: 3 residues within 4Å: Chain A: A.385, F.386 Ligands: D12.6 No protein-ligand interaction detected (PLIP) D12.6: 8 residues within 4Å: Chain A: I.19, A.22, G.378, A.381, V.382, A.385, F.386 Ligands: D12.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.19, A:A.22, A:A.381, A:A.385, A:F.386 D12.7: 6 residues within 4Å: Chain A: F.458, I.472, V.475, S.476, A.479 Ligands: PTY.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.458, A:F.458, A:I.472, A:A.479 D12.14: 7 residues within 4Å: Chain B: F.458 Chain C: L.25, K.29 Ligands: PTY.13, D12.15, D12.23, D12.24 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.458, B:F.458, C:L.25, C:K.29 D12.15: 6 residues within 4Å: Chain B: F.458 Ligands: PTY.12, PTY.13, D12.14, D12.23, D12.24 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.458 D12.16: 10 residues within 4Å: Chain B: M.1, P.2, Q.439, V.443, A.479, V.482, L.483, L.486 Ligands: PTY.10, PTY.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:M.1, B:V.443, B:A.479, B:V.482, B:L.483, B:L.483, B:L.483 D12.17: 3 residues within 4Å: Ligands: PTY.10, PTY.11, D12.26 No protein-ligand interaction detected (PLIP) D12.22: 3 residues within 4Å: Chain C: F.386, L.483 Ligands: PTY.21 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.386, C:L.483 D12.23: 7 residues within 4Å: Chain C: L.25, K.29, A.384, A.385 Ligands: D12.14, D12.15, D12.24 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.25, C:K.29, C:A.384 D12.24: 10 residues within 4Å: Chain C: A.22, L.25, A.381, V.382, A.384, A.385 Ligands: PTY.13, D12.14, D12.15, D12.23 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.25, C:A.381, C:V.382, C:A.384, C:A.385 D12.25: 5 residues within 4Å: Chain C: F.11, I.15, I.18 Ligands: PTY.18, PTY.20 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.15, C:I.18 D12.26: 4 residues within 4Å: Ligands: D12.17, PTY.18, PTY.19, PTY.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trinh, T.K.H. et al., pH-tunable membrane-active polymers, NCMNP2a- x , and their potential membrane protein applications. Chem Sci (2023)

Release Date

2022-08-17

Peptides

Multidrug efflux pump subunit AcrB: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Membrane

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

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