SMTL ID : 8zkp.1

Cryo-EM structure of the efflux transporter MmpL5/MmpS5 from Mycobacterium tuberculosis, C3 symmetry

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 19 residues within 4Å: Chain A: V.398, L.402, V.799, A.802, V.803, V.805, G.806, I.929, L.932, L.933, W.936 Chain D: G.391, P.392, V.395, V.398, A.399, L.932 Ligands: PEV.3, CDL.6 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:V.398, A:V.398, A:L.402, A:A.802, A:V.803, A:V.805, A:I.929, A:L.933, D:V.395, D:A.399, D:L.932 CDL.2: 25 residues within 4Å: Chain A: M.218, L.221, R.224, R.372, R.375, G.378, W.379, K.381, V.382, A.385, I.393, L.400, L.818, T.882, L.886, F.890, M.893, S.894, L.915, F.916, L.919, I.920, F.924 Chain C: L.42 Ligands: PEV.14 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.379, A:V.382, A:A.385, A:I.393, A:L.400, A:L.818, A:L.886, A:L.915, A:L.919, A:I.920, A:F.924, A:F.924, A:F.924, A:F.924, C:L.42 Hydrogen bonds: A:R.224 Salt bridges: A:R.375, A:R.375, A:R.375, A:K.381, A:K.381 CDL.6: 16 residues within 4Å: Chain D: V.398, V.799, A.802, V.803, G.806, I.929, L.932, L.933, W.936 Chain G: P.392, L.394, V.395, L.402, L.932 Ligands: CDL.1, CDL.11 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain G Hydrophobic interactions: D:V.398, D:V.398, D:V.799, D:V.803, D:I.929, D:I.929, D:L.932, D:L.932, D:L.933, D:L.933, G:L.394, G:V.395, G:L.402, G:L.932 CDL.7: 22 residues within 4Å: Chain D: M.218, L.221, V.222, A.374, R.375, G.378, W.379, V.382, A.385, I.393, L.400, L.818, L.886, F.890, L.915, F.916, L.919, I.920, F.924 Chain F: L.42 Ligands: PEV.3, PN7.10 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:L.221, D:W.379, D:A.385, D:I.393, D:L.400, D:L.818, D:L.886, D:F.890, D:F.890, D:L.919, D:L.919, D:I.920, D:F.924, D:F.924, D:F.924 Hydrogen bonds: D:R.224, D:A.374 Salt bridges: D:R.375, D:R.375, D:K.381, D:K.381 CDL.11: 17 residues within 4Å: Chain A: P.392, V.395, V.398, A.399, L.932 Chain G: V.398, L.402, V.799, A.802, V.803, V.805, G.806, L.810, L.932, L.933, W.936 Ligands: CDL.6 14 PLIP interactions: 9 interactions with chain G, 5 interactions with chain A Hydrophobic interactions: G:V.398, G:V.398, G:L.402, G:V.799, G:V.803, G:V.805, G:L.810, G:L.933, A:V.395, A:V.395, A:V.398, A:A.399, A:L.932 Hydrogen bonds: G:W.936 CDL.12: 25 residues within 4Å: Chain G: M.218, R.224, A.374, R.375, G.378, W.379, K.381, V.382, A.385, I.393, L.818, S.879, T.882, A.883, L.886, F.890, M.893, M.912, F.916, L.919, I.920, F.924 Chain I: L.42 Ligands: PEV.9, PN7.15 18 PLIP interactions: 17 interactions with chain G, 1 interactions with chain I Hydrophobic interactions: G:W.379, G:A.385, G:I.393, G:L.818, G:F.890, G:F.890, G:L.919, G:I.920, G:F.924, G:F.924, I:L.42 Hydrogen bonds: G:R.224, G:A.374, G:A.883 Salt bridges: 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.3: 15 residues within 4Å: Chain A: R.796, V.798, W.939, P.940, Q.941 Chain B: K.6, W.9, L.13, V.17 Chain D: G.396, A.399, L.400, V.403 Ligands: CDL.1, CDL.7 11 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: B:W.9, B:W.9, B:L.13, B:L.13, B:V.17, A:V.798, A:V.798, A:W.939, D:L.400, D:V.403 Hydrogen bonds: A:Q.941 PEV.4: 14 residues within 4Å: Chain A: I.24, G.304, A.307, H.308, L.311, L.315, T.316, L.351, T.352, L.786, I.790, I.793, T.794, R.796 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.24, A:A.307, A:H.308, A:L.315, A:L.351, A:T.352, A:L.786, A:I.793 Salt bridges: A:H.308, A:H.308, A:R.796 PEV.8: 9 residues within 4Å: Chain D: G.304, H.308, L.311, L.315, A.318, L.351, T.352, I.790, T.794 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:H.308, D:L.311, D:L.315, D:T.352, D:I.790 Salt bridges: D:H.308, D:H.308, D:H.308, D:R.796 PEV.9: 13 residues within 4Å: Chain D: C.785, F.788, R.796, V.798, W.939, P.940, Q.941 Chain E: K.6, W.9, V.17 Chain G: A.399, L.400 Ligands: CDL.12 8 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E, 2 interactions with chain G Hydrophobic interactions: D:F.788, D:V.798, D:W.939, E:W.9, E:V.17, G:A.399, G:L.400 Salt bridges: E:K.6 PEV.13: 15 residues within 4Å: Chain G: I.24, G.304, H.308, L.311, L.315, V.344, V.347, A.348, L.351, T.352, L.786, I.790, I.793, T.794, R.796 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:I.24, G:H.308, G:L.315, G:L.315, G:L.315, G:V.344, G:V.347, G:A.348, G:L.351, G:T.352, G:L.786 Salt bridges: G:H.308, G:H.308, G:H.308, G:R.796 PEV.14: 15 residues within 4Å: Chain A: A.399, L.400 Chain G: F.788, R.796, V.798, W.939, P.940, Q.941 Chain H: K.6, W.9, L.13, V.16, V.17, I.20 Ligands: CDL.2 14 PLIP interactions: 6 interactions with chain H, 5 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: H:W.9, H:L.13, H:V.16, H:V.17, H:I.20, G:F.788, G:V.798, G:V.798, G:W.939, A:A.399, A:L.400, A:L.400 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)(Non-covalent)

PN7.5: 6 residues within 4Å: Chain A: W.389, P.392 Chain C: S.41 Chain G: W.936, W.939, V.942 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain A, 1 interactions with chain G Salt bridges: H:K.6 Hydrophobic interactions: A:W.389, G:W.936 PN7.10: 6 residues within 4Å: Chain A: W.936, W.939, V.942 Chain D: W.389 Chain F: S.41 Ligands: CDL.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.6 Hydrophobic interactions: A:W.936 PN7.15: 8 residues within 4Å: Chain D: W.936, W.939 Chain E: K.6 Chain G: W.389, P.392, I.393 Chain I: S.41 Ligands: CDL.12 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: D:W.936, G:W.389 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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