SMTL ID : 9qpr.1

Single particle cryo-EM structure of the multidrug efflux pump MdtF from Escherichia coli

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

PTY.1: 13 residues within 4Å: Chain A: Y.4, I.18, A.22, A.26, A.381, S.384, A.385 Ligands: PTY.2, PTY.3, PTY.7, PTY.8, PTY.9, PTY.16 Ligand excluded by PLIP PTY.2: 8 residues within 4Å: Chain A: Y.4 Ligands: PTY.1, D12.5, PTY.10, PTY.16, D12.17, PTY.18, PTY.21 Ligand excluded by PLIP PTY.3: 9 residues within 4Å: Chain A: A.385, V.386 Chain B: F.458 Ligands: PTY.1, PTY.4, PTY.7, PTY.8, PTY.9, D12.25 Ligand excluded by PLIP PTY.4: 6 residues within 4Å: Ligands: PTY.3, PTY.8, PTY.13, PTY.14, PTY.15, D12.25 Ligand excluded by PLIP PTY.7: 16 residues within 4Å: Chain A: I.382, V.386, M.454, F.458, R.468, I.472, L.479, F.483 Chain C: I.18, L.25 Ligands: PTY.1, PTY.3, D12.6, PTY.8, PTY.24, PTY.26 Ligand excluded by PLIP PTY.8: 7 residues within 4Å: Ligands: PTY.1, PTY.3, PTY.4, PTY.7, PTY.24, D12.25, PTY.28 Ligand excluded by PLIP PTY.9: 15 residues within 4Å: Chain A: I.18, L.21, L.25 Chain B: V.447, M.454, P.455, F.458, M.459, I.877, V.881, A.885, A.888 Ligands: PTY.1, PTY.3, PTY.16 Ligand excluded by PLIP PTY.10: 6 residues within 4Å: Ligands: PTY.2, PTY.14, PTY.18, PTY.19, PTY.20, PTY.21 Ligand excluded by PLIP PTY.11: 13 residues within 4Å: Chain B: M.19, L.21, A.22, L.25, N.29, S.384, A.385 Chain C: M.454, F.458, M.459, Q.870, L.874 Ligands: PTY.13 Ligand excluded by PLIP PTY.13: 7 residues within 4Å: Chain B: A.385, V.386 Ligands: PTY.4, PTY.11, PTY.14, PTY.15, PTY.27 Ligand excluded by PLIP PTY.14: 8 residues within 4Å: Ligands: PTY.4, PTY.10, D12.12, PTY.13, PTY.15, D12.25, PTY.27, PTY.28 Ligand excluded by PLIP PTY.15: 12 residues within 4Å: Chain B: V.386, F.388, M.454, A.457, F.458, R.468, I.472 Ligands: PTY.4, D12.12, PTY.13, PTY.14, PTY.18 Ligand excluded by PLIP PTY.16: 11 residues within 4Å: Chain A: Y.4, R.8 Chain B: Q.439, R.440, L.889, E.891 Ligands: PTY.1, PTY.2, PTY.9, D12.17, PTY.18 Ligand excluded by PLIP PTY.18: 19 residues within 4Å: Chain B: A.2, Y.4, F.5, L.15, I.382, Q.439, I.472, S.476, L.479, L.480, V.482, M.486 Ligands: PTY.2, PTY.10, D12.12, PTY.15, PTY.16, D12.17, PTY.19 Ligand excluded by PLIP PTY.19: 7 residues within 4Å: Chain B: R.8 Chain C: Q.439, R.440 Ligands: PTY.10, PTY.18, PTY.20, PTY.21 Ligand excluded by PLIP PTY.20: 9 residues within 4Å: Chain C: A.2, Y.4, Q.439, M.486 Ligands: PTY.10, PTY.19, PTY.21, D12.22, PTY.27 Ligand excluded by PLIP PTY.21: 10 residues within 4Å: Chain C: N.3, Y.4 Ligands: PTY.2, D12.5, D12.6, PTY.10, PTY.19, PTY.20, D12.22, PTY.26 Ligand excluded by PLIP PTY.24: 12 residues within 4Å: Chain C: M.19, A.22, A.381, S.384, A.385, L.480 Ligands: PTY.7, PTY.8, D12.22, D12.25, PTY.27, PTY.28 Ligand excluded by PLIP PTY.26: 18 residues within 4Å: Chain A: R.440, V.447, A.451, M.454, I.877, S.878, V.881, A.885, A.888, L.889 Chain C: R.8, F.11, V.14 Ligands: D12.5, D12.6, PTY.7, PTY.21, D12.22 Ligand excluded by PLIP PTY.27: 17 residues within 4Å: Chain C: I.382, V.386, F.388, F.458, E.465, R.468, I.472, I.475, L.479, V.482, F.483 Ligands: PTY.13, PTY.14, PTY.20, D12.23, PTY.24, PTY.28 Ligand excluded by PLIP PTY.28: 7 residues within 4Å: Chain C: A.385, V.386 Ligands: PTY.8, PTY.14, PTY.24, D12.25, PTY.27 Ligand excluded by PLIP

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

D12.5: 8 residues within 4Å: Chain A: N.3, Q.439, V.443, M.486 Ligands: PTY.2, D12.6, PTY.21, PTY.26 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.443 D12.6: 4 residues within 4Å: Ligands: D12.5, PTY.7, PTY.21, PTY.26 No protein-ligand interaction detected (PLIP) D12.12: 4 residues within 4Å: Chain B: L.479 Ligands: PTY.14, PTY.15, PTY.18 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.479 D12.17: 3 residues within 4Å: Ligands: PTY.2, PTY.16, PTY.18 No protein-ligand interaction detected (PLIP) D12.22: 8 residues within 4Å: Chain C: Y.4, F.5, F.11, L.15 Ligands: PTY.20, PTY.21, PTY.24, PTY.26 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.4, C:F.5, C:F.11, C:L.15 D12.23: 6 residues within 4Å: Chain B: F.11, I.18 Chain C: R.440, V.447, A.888 Ligands: PTY.27 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.11, B:I.18, C:V.447 D12.25: 6 residues within 4Å: Ligands: PTY.3, PTY.4, PTY.8, PTY.14, PTY.24, PTY.28 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lawrence, R. et al., Molecular basis for multidrug efflux by an anaerobic RND transporter. Biorxiv (2025)

Release Date

2025-05-14

Peptides

Multidrug resistance protein MdtF: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Membrane

We predict this structure to be a membrane protein.
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Multidrug resistance protein MdtF