SMTL ID : 9qpt.1

Single particle cryo-EM structure of MdtF V610F with bound Rhodamine 6G

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

D12.1: 7 residues within 4Å: Chain A: M.454, A.457, I.472, L.479 Ligands: PTY.3, PTY.5, D12.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.457, A:I.472, A:L.479 D12.10: 7 residues within 4Å: Ligands: D12.1, PTY.3, PTY.8, D12.26, PTY.31, D12.34, PTY.35 No protein-ligand interaction detected (PLIP) D12.11: 7 residues within 4Å: Chain A: L.15, I.18, A.22 Ligands: PTY.2, PTY.6, PTY.12, PTY.19 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.15, A:I.18, A:A.22 D12.20: 6 residues within 4Å: Chain B: I.382, L.479, L.480 Ligands: PTY.14, PTY.16, D12.25 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.382, B:L.479, B:L.480 D12.21: 8 residues within 4Å: Chain B: A.2, M.486 Ligands: PTY.2, PTY.12, PTY.18, D12.22, D12.25, D12.26 No protein-ligand interaction detected (PLIP) D12.22: 7 residues within 4Å: Chain B: V.443, S.450, L.479 Ligands: PTY.12, PTY.14, D12.21, D12.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.443, B:L.479 D12.23: 2 residues within 4Å: Ligands: PTY.13, PTY.28 No protein-ligand interaction detected (PLIP) D12.24: 3 residues within 4Å: Ligands: PTY.13, PTY.15, PTY.28 No protein-ligand interaction detected (PLIP) D12.25: 7 residues within 4Å: Chain B: L.479, V.482, F.483, M.486 Ligands: D12.20, D12.21, D12.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.482 D12.26: 4 residues within 4Å: Ligands: D12.10, PTY.17, PTY.18, D12.21 No protein-ligand interaction detected (PLIP) D12.34: 4 residues within 4Å: Ligands: D12.10, PTY.17, PTY.31, PTY.35 No protein-ligand interaction detected (PLIP) D12.36: 4 residues within 4Å: Chain C: Y.4, F.5 Ligands: PTY.31, PTY.35 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.5, C:F.5

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

PTY.2: 12 residues within 4Å: Chain A: N.3, Y.4, F.5, D.7, R.8, F.483 Ligands: PTY.8, D12.11, PTY.12, PTY.17, PTY.18, D12.21 Ligand excluded by PLIP PTY.3: 21 residues within 4Å: Chain A: I.382, Q.439, V.443, I.472, I.475, S.476, L.479, L.480, F.483, M.486, A.885, A.888, L.889 Chain C: R.8, F.11 Ligands: D12.1, PTY.4, PTY.5, PTY.8, D12.10, PTY.35 Ligand excluded by PLIP PTY.4: 13 residues within 4Å: Chain A: V.447, A.451, M.454, F.458, M.459, S.460, I.877, V.881 Chain C: L.25, N.29 Ligands: PTY.3, PTY.7, PTY.32 Ligand excluded by PLIP PTY.5: 11 residues within 4Å: Chain A: V.386, G.387, F.388, A.457, F.458, R.468, I.472 Ligands: D12.1, PTY.3, PTY.6, PTY.7 Ligand excluded by PLIP PTY.6: 15 residues within 4Å: Chain A: A.22, L.25, A.26, A.381, I.382, S.384, A.385 Ligands: PTY.5, PTY.7, PTY.9, D12.11, PTY.14, PTY.16, PTY.19, PTY.33 Ligand excluded by PLIP PTY.7: 6 residues within 4Å: Chain A: F.458 Ligands: PTY.4, PTY.5, PTY.6, PTY.32, PTY.33 Ligand excluded by PLIP PTY.8: 10 residues within 4Å: Chain A: A.2, N.3, Y.4, F.5, F.483, M.486 Ligands: PTY.2, PTY.3, D12.10, PTY.35 Ligand excluded by PLIP PTY.9: 10 residues within 4Å: Chain A: L.25, N.29, S.384, A.385 Chain B: F.458, Q.870 Ligands: PTY.6, PTY.14, PTY.16, PTY.19 Ligand excluded by PLIP PTY.12: 18 residues within 4Å: Chain A: F.11, I.18 Chain B: Q.439, R.440, V.443, G.444, V.447, M.454, V.881, A.885, A.888, L.889 Ligands: PTY.2, D12.11, PTY.18, PTY.19, D12.21, D12.22 Ligand excluded by PLIP PTY.13: 10 residues within 4Å: Chain B: N.3, Y.4, F.5, R.8, L.15 Ligands: PTY.17, D12.23, D12.24, PTY.28, PTY.31 Ligand excluded by PLIP PTY.14: 13 residues within 4Å: Chain B: V.386, F.388, M.454, A.457, F.458, R.468, I.472 Ligands: PTY.6, PTY.9, PTY.16, D12.20, D12.22, PTY.33 Ligand excluded by PLIP PTY.15: 10 residues within 4Å: Chain B: A.22, N.29, S.384, A.385 Chain C: F.458 Ligands: PTY.16, D12.24, PTY.28, PTY.29, PTY.33 Ligand excluded by PLIP PTY.16: 11 residues within 4Å: Chain B: M.19, A.22, I.382, A.385, V.386 Ligands: PTY.6, PTY.9, PTY.14, PTY.15, D12.20, PTY.33 Ligand excluded by PLIP PTY.17: 7 residues within 4Å: Chain B: N.3 Ligands: PTY.2, PTY.13, PTY.18, D12.26, PTY.31, D12.34 Ligand excluded by PLIP PTY.18: 11 residues within 4Å: Chain A: Y.4, R.8 Chain B: A.2, Q.439, R.440, K.953 Ligands: PTY.2, PTY.12, PTY.17, D12.21, D12.26 Ligand excluded by PLIP PTY.19: 14 residues within 4Å: Chain A: A.22, L.25 Chain B: M.454, P.455, F.458, A.873, L.874, I.877, S.878, V.881 Ligands: PTY.6, PTY.9, D12.11, PTY.12 Ligand excluded by PLIP PTY.28: 16 residues within 4Å: Chain B: Y.4, F.11, I.18 Chain C: R.440, V.443, V.447, A.885, A.888, L.889 Ligands: PTY.13, PTY.15, D12.23, D12.24, PTY.29, PTY.30, PTY.31 Ligand excluded by PLIP PTY.29: 14 residues within 4Å: Chain B: L.25 Chain C: A.451, M.454, P.455, F.458, S.460, Q.870, L.874, I.877, S.878, V.881 Ligands: PTY.15, PTY.28, PTY.30 Ligand excluded by PLIP PTY.30: 21 residues within 4Å: Chain C: I.382, V.386, F.388, V.443, S.450, M.454, A.457, F.458, R.468, I.472, I.475, S.476, L.479, L.480, V.482, M.486 Ligands: PTY.28, PTY.29, PTY.31, PTY.32, PTY.33 Ligand excluded by PLIP PTY.31: 10 residues within 4Å: Chain C: A.2, N.3 Ligands: D12.10, PTY.13, PTY.17, PTY.28, PTY.30, D12.34, PTY.35, D12.36 Ligand excluded by PLIP PTY.32: 11 residues within 4Å: Chain C: I.18, L.21, A.22, I.382, A.385, V.386, F.388 Ligands: PTY.4, PTY.7, PTY.30, PTY.33 Ligand excluded by PLIP PTY.33: 7 residues within 4Å: Ligands: PTY.6, PTY.7, PTY.14, PTY.15, PTY.16, PTY.30, PTY.32 Ligand excluded by PLIP PTY.35: 8 residues within 4Å: Chain C: Y.4, R.8 Ligands: PTY.3, PTY.8, D12.10, PTY.31, D12.34, D12.36 Ligand excluded by PLIP

1 x RHQ: RHODAMINE 6G(Non-covalent)

RHQ.27: 13 residues within 4Å: Chain C: S.134, I.136, V.139, F.178, T.277, P.326, Y.327, M.571, F.610, F.613, F.615, F.626, L.666 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.136, C:V.139, C:T.277, C:P.326, C:Y.327, C:F.613, C:L.666 pi-Stacking: C:F.178, C:F.178, C:F.626

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
A

B
B

C
C

Membrane

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

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