SMTL ID : 9qps.1

Single particle cryo-EM structure of MdtF V610F

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

PTY.1: 11 residues within 4Å: Chain A: A.26, S.384, A.385, V.386, G.387 Chain B: M.454, F.458 Ligands: PTY.7, PTY.12, PTY.19, PTY.23 Ligand excluded by PLIP PTY.2: 10 residues within 4Å: Chain A: P.455, F.458, M.459, S.460, A.873, I.877, V.881 Chain C: L.25 Ligands: PTY.5, PTY.8 Ligand excluded by PLIP PTY.3: 10 residues within 4Å: Chain A: Q.439, F.483 Ligands: D12.4, PTY.5, D12.6, PTY.9, D12.10, PTY.21, D12.30, PTY.33 Ligand excluded by PLIP PTY.5: 17 residues within 4Å: Chain A: Q.439, V.443, V.447, A.451, M.454, L.479, A.885, A.888, L.889 Chain C: F.11, V.14, I.18 Ligands: PTY.2, PTY.3, D12.4, D12.6, PTY.33 Ligand excluded by PLIP PTY.7: 16 residues within 4Å: Chain A: I.382, A.385, V.386, F.388, R.468, I.472, I.475, S.476, L.479, L.480, F.483 Ligands: PTY.1, D12.4, D12.6, PTY.8, PTY.23 Ligand excluded by PLIP PTY.8: 14 residues within 4Å: Chain A: T.96, G.97, A.457, F.458, S.460, G.461, R.468 Chain C: A.385 Ligands: PTY.2, PTY.7, PTY.23, PTY.25, PTY.29, D12.31 Ligand excluded by PLIP PTY.9: 12 residues within 4Å: Chain A: N.3, Y.4, F.5, D.7, R.8, F.483 Ligands: PTY.3, D12.10, PTY.12, PTY.13, PTY.20, PTY.21 Ligand excluded by PLIP PTY.12: 14 residues within 4Å: Chain A: I.18, L.25 Chain B: A.451, M.454, P.455, F.458, Q.870, L.874, I.877, V.881 Ligands: PTY.1, PTY.9, PTY.13, D12.18 Ligand excluded by PLIP PTY.13: 15 residues within 4Å: Chain A: F.11, V.14, I.18 Chain B: Q.439, R.440, V.443, G.444, V.447, A.885, A.888, L.889 Ligands: PTY.9, PTY.12, D12.18, PTY.20 Ligand excluded by PLIP PTY.14: 18 residues within 4Å: Chain B: I.18, L.25, N.29 Chain C: V.447, S.450, A.451, M.454, F.458, Q.870, L.874, I.877, V.881 Ligands: D12.15, PTY.16, PTY.17, PTY.26, PTY.27, D12.28 Ligand excluded by PLIP PTY.16: 12 residues within 4Å: Chain B: M.19, A.22, A.26, A.381, I.382, S.384, A.385, L.480 Ligands: PTY.14, D12.15, PTY.17, PTY.19 Ligand excluded by PLIP PTY.17: 7 residues within 4Å: Chain B: A.385, V.386 Ligands: PTY.14, D12.15, PTY.16, PTY.19, PTY.26 Ligand excluded by PLIP PTY.19: 16 residues within 4Å: Chain B: I.382, V.386, F.388, M.454, F.458, R.468, I.472, I.475, L.479, F.483 Ligands: PTY.1, PTY.16, PTY.17, D12.18, PTY.20, PTY.23 Ligand excluded by PLIP PTY.20: 10 residues within 4Å: Chain B: A.2, Y.4 Ligands: PTY.9, D12.10, PTY.13, D12.18, PTY.19, PTY.21, PTY.22, D12.24 Ligand excluded by PLIP PTY.21: 8 residues within 4Å: Ligands: PTY.3, PTY.9, D12.10, PTY.20, PTY.22, D12.24, D12.30, D12.32 Ligand excluded by PLIP PTY.22: 6 residues within 4Å: Chain B: Y.4 Ligands: PTY.20, PTY.21, D12.24, PTY.27, D12.32 Ligand excluded by PLIP PTY.23: 8 residues within 4Å: Chain B: F.458 Ligands: PTY.1, PTY.7, PTY.8, D12.11, D12.18, PTY.19, PTY.29 Ligand excluded by PLIP PTY.25: 10 residues within 4Å: Chain C: M.19, I.382, A.385, V.386, L.479 Ligands: PTY.8, PTY.26, PTY.27, PTY.29, D12.31 Ligand excluded by PLIP PTY.26: 15 residues within 4Å: Chain C: I.382, V.443, S.450, M.454, F.458, R.468, I.472, I.475, S.476, L.479, L.480 Ligands: PTY.14, PTY.17, PTY.25, PTY.33 Ligand excluded by PLIP PTY.27: 16 residues within 4Å: Chain B: R.8, F.11, L.15 Chain C: Q.439, R.440, V.443, M.486, A.885, A.888, L.889 Ligands: PTY.14, PTY.22, D12.24, PTY.25, D12.28, D12.32 Ligand excluded by PLIP PTY.29: 4 residues within 4Å: Ligands: PTY.8, PTY.23, PTY.25, D12.31 Ligand excluded by PLIP PTY.33: 9 residues within 4Å: Chain C: N.3, Y.4, F.5, L.15 Ligands: PTY.3, PTY.5, PTY.26, D12.30, D12.32 Ligand excluded by PLIP

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

D12.4: 6 residues within 4Å: Chain A: M.454, L.479 Ligands: PTY.3, PTY.5, D12.6, PTY.7 No protein-ligand interaction detected (PLIP) D12.6: 8 residues within 4Å: Chain A: Q.439, L.479, V.482, M.486 Ligands: PTY.3, D12.4, PTY.5, PTY.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.479, A:V.482 D12.10: 4 residues within 4Å: Ligands: PTY.3, PTY.9, PTY.20, PTY.21 No protein-ligand interaction detected (PLIP) D12.11: 1 residues within 4Å: Ligands: PTY.23 No protein-ligand interaction detected (PLIP) D12.15: 8 residues within 4Å: Chain B: I.18, L.21, L.25 Chain C: I.877, V.881 Ligands: PTY.14, PTY.16, PTY.17 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.18, B:L.21, B:L.25, C:I.877, C:V.881 D12.18: 9 residues within 4Å: Chain B: A.446, V.447, S.450, M.454 Ligands: PTY.12, PTY.13, PTY.19, PTY.20, PTY.23 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.446, B:V.447 D12.24: 5 residues within 4Å: Ligands: PTY.20, PTY.21, PTY.22, PTY.27, D12.28 No protein-ligand interaction detected (PLIP) D12.28: 3 residues within 4Å: Ligands: PTY.14, D12.24, PTY.27 No protein-ligand interaction detected (PLIP) D12.30: 3 residues within 4Å: Ligands: PTY.3, PTY.21, PTY.33 No protein-ligand interaction detected (PLIP) D12.31: 3 residues within 4Å: Ligands: PTY.8, PTY.25, PTY.29 No protein-ligand interaction detected (PLIP) D12.32: 4 residues within 4Å: Ligands: PTY.21, PTY.22, PTY.27, PTY.33 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
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Multidrug resistance protein MdtF

Related Entries With Identical Sequence