SMTL ID : 8g0b.1

Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase FO region

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-9-1-1-1-mer

Ligands

7 x YGR: (1R,2S)-1-(6-bromo-2-methoxyquinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2,3,6-trimethoxypyridin-4-yl)butan-2-ol(Non-covalent)

YGR.1: 16 residues within 4Å: Chain A: G.62, E.65, A.66, Y.68, F.69, L.72 Chain B: L.63, A.66, A.67, I.70, F.74 Chain J: L.170, P.172, I.173, V.176 Ligands: YGR.7 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.70, A:A.66, A:F.69, A:F.69 Salt bridges: A:E.65 YGR.2: 15 residues within 4Å: Chain D: G.62, E.65, A.66, Y.68, F.69, L.72 Chain E: L.63, A.66, A.67, I.70 Chain J: F.213, P.214, W.218, F.221 Ligands: YGR.3 8 PLIP interactions: 5 interactions with chain D, 2 interactions with chain J, 1 interactions with chain E Hydrophobic interactions: D:E.65, D:F.69, D:F.69, D:F.69, J:F.221, E:I.70 Salt bridges: D:E.65 pi-Stacking: J:F.221 YGR.3: 12 residues within 4Å: Chain E: G.62, E.65, A.66, Y.68, F.69, L.72 Chain F: L.63, A.66, A.67, I.70 Ligands: YGR.2, YGR.4 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:E.65, E:A.66, E:F.69, E:F.69, E:L.72, F:I.70 Salt bridges: E:E.65 YGR.4: 11 residues within 4Å: Chain F: G.62, E.65, A.66, F.69, L.72 Chain G: L.63, A.66, A.67, I.70 Ligands: YGR.3, YGR.5 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:A.66, F:F.69, F:F.69, F:L.72, G:I.70 Salt bridges: F:E.65 YGR.5: 13 residues within 4Å: Chain G: G.62, E.65, A.66, Y.68, F.69, L.72 Chain H: L.63, A.66, A.67, I.70, F.74 Ligands: YGR.4, YGR.6 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:E.65, G:F.69 Salt bridges: G:E.65 YGR.6: 10 residues within 4Å: Chain H: G.62, E.65, A.66, Y.68, F.69, L.72 Chain I: A.66, A.67, I.70 Ligands: YGR.5 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:E.65, H:A.66, H:F.69, H:F.69 Salt bridges: H:E.65 YGR.7: 11 residues within 4Å: Chain A: L.63, A.66, A.67, I.70 Chain I: G.62, E.65, A.66, Y.68, F.69, L.72 Ligands: YGR.1 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:E.65, I:A.66, I:F.69, I:F.69 Salt bridges: I:E.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Courbon, G.M. et al., Mechanism of mycobacterial ATP synthase inhibition by squaramides and second generation diarylquinolines. Embo J. (2023)

Release Date

2023-02-15

Peptides

ATP synthase subunit c: ABCDEFGHI
ATP synthase subunit a: J
ATP synthase subunit b: K
ATP synthase subunit b-delta: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
7

H
8

I
9

J
a

K
b

L
d

Membrane

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

ATP synthase subunit a

ATP synthase subunit b

ATP synthase subunit b-delta

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