SMTL ID : 7jgc.1

Cryo-EM structure of bedaquiline-saturated Mycobacterium smegmatis ATP synthase FO region

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-9-mer

Ligands

7 x BQ1: Bedaquiline(Non-covalent)

BQ1.1: 14 residues within 4Å: Chain A: P.172, I.173, V.176 Chain D: A.28, G.62, E.65, A.66, Y.68, F.69, L.72 Chain E: L.63, A.66, A.67 Ligands: BQ1.7 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.69, D:F.69, D:L.72, A:P.172, A:P.172, A:V.176 Salt bridges: D:D.32, D:E.65 BQ1.2: 11 residues within 4Å: Chain A: F.213, V.217, F.221 Chain G: G.62, E.65, A.66, Y.68, F.69 Chain H: L.63, A.66, I.70 7 PLIP interactions: 3 interactions with chain A, 1 interactions with chain H, 3 interactions with chain G Hydrophobic interactions: A:F.213, A:V.217, A:F.221, H:I.70, G:E.65, G:F.69 Salt bridges: G:E.65 BQ1.3: 9 residues within 4Å: Chain H: G.62, E.65, A.66, Y.68, F.69 Chain I: L.63, A.67, I.70 Ligands: BQ1.4 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:E.65 Salt bridges: H:E.65 Hydrophobic interactions: I:I.70 BQ1.4: 8 residues within 4Å: Chain I: G.62, E.65, A.66, Y.68 Chain J: A.66, A.67, I.70 Ligands: BQ1.3 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:A.66, J:I.70 Salt bridges: I:E.65 BQ1.5: 8 residues within 4Å: Chain J: G.62, E.65, A.66, Y.68, F.69 Chain K: A.66, A.67, I.70 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:E.65, J:F.69, J:F.69 Hydrogen bonds: J:E.65 Salt bridges: J:E.65 pi-Stacking: J:F.69 BQ1.6: 9 residues within 4Å: Chain K: G.62, E.65, A.66, Y.68, F.69 Chain L: A.66, A.67, I.70 Ligands: BQ1.7 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:F.69, K:F.69, L:I.70 Hydrogen bonds: K:E.65 Salt bridges: K:E.65 BQ1.7: 11 residues within 4Å: Chain D: L.63, A.66, A.67, I.70 Chain L: G.62, E.65, A.66, Y.68, F.69 Ligands: BQ1.1, BQ1.6 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain D Hydrophobic interactions: L:A.66, L:F.69, D:I.70 Salt bridges: L:E.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, H. et al., Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline. Nature (2021)

Release Date

2020-08-19

Peptides

ATP synthase subunit a: A
ATP synthase subunit b: B
ATP synthase subunit b-delta: C
ATP synthase subunit c: DEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
b

C
d

D
1

E
2

F
3

G
4

H
5

I
6

J
7

K
8

L
9

Membrane

We predict this structure to be a membrane protein.
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ATP synthase subunit a

ATP synthase subunit b

ATP synthase subunit b-delta

ATP synthase subunit c

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