SMTL ID : 8zkq.1

Cryo-EM structure of the efflux transporter MmpL5/MmpS5 from Mycobacterium tuberculosis, C1 symmetry

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 20 residues within 4Å: Chain A: V.398, L.402, L.405, F.788, V.799, A.802, V.803, V.805, G.806, L.932, L.933, W.936 Chain D: P.392, L.394, V.395, V.398, A.399 Ligands: CDL.2, PEV.5, CDL.7 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:V.398, A:L.402, A:L.405, A:F.788, A:V.799, A:A.802, A:V.803, A:V.805, A:L.932, A:L.933, D:L.394, D:V.395, D:V.398, D:A.399 CDL.2: 19 residues within 4Å: Chain A: P.392, V.395, V.398, A.399 Chain G: L.394, V.398, L.402, V.799, A.802, V.803, V.805, G.806, V.809, L.810, L.932, L.933, W.936 Ligands: CDL.1, CDL.7 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain A Hydrophobic interactions: G:L.394, G:V.398, G:V.398, G:L.402, G:V.799, G:V.803, G:V.805, G:L.810, G:L.810, G:L.933, A:V.395, A:V.398 CDL.3: 27 residues within 4Å: Chain A: V.214, M.218, L.221, V.222, R.372, A.374, R.375, G.378, W.379, K.381, V.382, A.385, L.400, L.818, T.882, L.886, F.890, M.893, V.897, L.915, F.916, L.919, I.920, F.924 Chain C: L.42 Ligands: PN7.6, PEV.14 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.214, A:W.379, A:V.382, A:A.385, A:L.400, A:L.818, A:L.886, A:F.890, A:V.897, A:L.915, A:F.924, C:L.42 Hydrogen bonds: A:T.882 Salt bridges: A:R.372, A:R.375, A:R.375, A:R.375, A:K.381, A:K.381 CDL.7: 16 residues within 4Å: Chain D: L.394, V.398, V.799, A.802, V.803, L.810, I.929, L.932, L.933, W.936 Chain G: P.392, V.395, L.402, L.932 Ligands: CDL.1, CDL.2 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain G Hydrophobic interactions: D:L.394, D:V.398, D:V.398, D:V.799, D:V.803, D:L.810, D:I.929, D:L.932, D:L.932, D:L.933, G:L.402, G:L.932 CDL.8: 20 residues within 4Å: Chain D: V.214, M.218, V.222, R.372, R.375, G.378, W.379, V.382, A.385, L.818, L.886, F.890, M.893, S.894, F.916, L.919, I.920, F.924 Chain F: L.42 Ligands: PEV.5 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:V.214, D:W.379, D:V.382, D:V.382, D:A.385, D:L.818, D:L.886, D:F.890, D:F.890, D:L.919, D:I.920, D:F.924, D:F.924, D:F.924, F:L.42 Salt bridges: D:R.224, D:R.372, D:R.375, D:R.375, D:K.381 CDL.12: 21 residues within 4Å: Chain G: M.218, L.221, R.372, A.374, R.375, G.378, W.379, K.381, V.382, A.385, I.393, L.400, L.818, T.882, L.886, F.890, L.919, I.920, F.924 Chain I: L.42 Ligands: PEV.9 20 PLIP interactions: 20 interactions with chain G Hydrophobic interactions: G:L.221, G:W.379, G:A.385, G:I.393, G:I.393, G:L.400, G:L.818, G:F.890, G:F.890, G:F.890, G:L.919, G:L.919, G:F.924, G:F.924, G:F.924 Salt bridges: G:R.372, G:R.375, G:R.375, G:K.381, G:K.381

6 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PEV.4: 6 residues within 4Å: Chain A: H.308, L.311, L.315, G.319, L.351, R.796 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.308, A:L.311, A:L.315, A:L.351 Salt bridges: A:H.308, A:H.308, A:R.796 PEV.5: 13 residues within 4Å: Chain A: V.798, W.939, P.940, Q.941 Chain B: W.9, I.10, L.13, I.20 Chain D: L.400, V.403 Ligands: CDL.1, CDL.8, PN7.11 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:V.403, B:W.9, B:L.13, B:I.20 Salt bridges: B:K.6 PEV.9: 13 residues within 4Å: Chain D: F.788, V.798, W.939, P.940, Q.941 Chain E: K.6, W.9, V.17 Chain G: A.399, L.400, V.403 Ligands: CDL.12, PN7.15 8 PLIP interactions: 3 interactions with chain G, 2 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: G:A.399, G:L.400, G:V.403, E:W.9, E:V.17, D:F.788, D:V.798, D:W.939 PEV.10: 10 residues within 4Å: Chain D: G.304, H.308, L.311, L.315, V.344, L.351, T.352, L.786, T.794, R.796 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.311, D:L.315, D:L.315, D:V.344, D:T.352, D:L.786 Salt bridges: D:H.308, D:H.308, D:R.796 PEV.13: 9 residues within 4Å: Chain G: I.24, H.308, L.311, L.315, L.351, L.786, I.790, T.794, R.796 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:H.308, G:L.311, G:L.315, G:L.351, G:L.786 Salt bridges: G:H.308, G:R.796 PEV.14: 14 residues within 4Å: Chain A: A.399, L.400 Chain G: R.796, V.798, W.939, P.940, Q.941 Chain H: K.6, W.9, L.13, V.16, V.17 Ligands: CDL.3, PN7.6 12 PLIP interactions: 1 interactions with chain A, 6 interactions with chain H, 5 interactions with chain G Hydrophobic interactions: A:L.400, H:W.9, H:W.9, H:L.13, H:V.16, H:V.17, G:V.798, G:W.939, G:W.939, G:W.939 Salt bridges: H:K.6 Hydrogen bonds: G:Q.941

3 x PN7: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide(Covalent)

PN7.6: 7 residues within 4Å: Chain A: W.389 Chain C: S.41 Chain G: W.936, W.939, V.942 Ligands: CDL.3, PEV.14 4 PLIP interactions: 1 interactions with chain H, 2 interactions with chain A, 1 interactions with chain G Salt bridges: H:K.6 Hydrophobic interactions: A:W.389, A:W.389, G:W.936 PN7.11: 9 residues within 4Å: Chain A: W.936, W.939, V.942 Chain D: W.389, P.392, I.393 Chain F: S.41, L.42 Ligands: PEV.5 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F, 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:W.936, F:L.42, D:W.389 Salt bridges: B:K.6 PN7.15: 8 residues within 4Å: Chain D: W.936, W.939, V.942 Chain E: K.6 Chain G: W.389 Chain I: S.41, L.42 Ligands: PEV.9 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain D, 1 interactions with chain I, 1 interactions with chain E Hydrophobic interactions: G:W.389, D:W.936, I:L.42 Salt bridges: E:K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, B. et al., Membrane transporter. To Be Published

Release Date

2025-05-21

Peptides

Siderophore exporter MmpL5: ADG
Siderophore export accessory protein MmpS5: BEH
Meromycolate extension acyl carrier protein: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
F

E
C

H
G

C
H

F
D

I
I

Membrane

We predict this structure to be a membrane protein.
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Siderophore exporter MmpL5

Siderophore export accessory protein MmpS5

Meromycolate extension acyl carrier protein

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