SMTL ID : 8g0e.1

Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase rotational state 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-1-9-1-mer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 15 residues within 4Å: Chain A: K.175, T.176, G.177, K.178, T.179, A.180, E.331, F.360, R.365, P.366, Q.433, Q.435 Chain F: D.357, Y.366 Ligands: MG.2 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:K.175, A:T.176, A:G.177, A:K.178, A:T.179, A:A.180, A:E.331, A:Q.433, A:Q.435, A:Q.435, F:D.357 Salt bridges: A:K.175, A:K.178, A:K.178 pi-Stacking: A:F.360 ATP.3: 13 residues within 4Å: Chain B: R.174, K.175, T.176, G.177, K.178, T.179, A.180, F.360, R.365, P.366, Q.433, Q.435 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.175, B:T.176, B:G.177, B:K.178, B:T.179, B:T.179, B:A.180, B:R.365, B:Q.433, B:Q.435, B:Q.435 Salt bridges: B:K.175, B:K.178, B:K.178 ATP.5: 14 residues within 4Å: Chain C: K.175, T.176, G.177, K.178, T.179, A.180, F.360, R.365, P.366, Q.433, P.434, Q.435 Chain E: Y.366 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:K.175, C:T.176, C:G.177, C:G.177, C:K.178, C:T.179, C:A.180, C:Q.433, C:Q.435 Salt bridges: C:K.175, C:K.178, C:K.178 pi-Stacking: C:F.360 ATP.7: 20 residues within 4Å: Chain B: S.347, V.374, R.376 Chain E: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, R.193, E.196, F.338, F.343, M.416, A.419, F.422, T.423 Ligands: MG.8 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain B Hydrogen bonds: E:G.161, E:G.163, E:V.164, E:G.165, E:K.166, E:T.167, E:T.167, E:V.168, B:R.376 Salt bridges: E:K.166, E:K.166, E:R.193, B:R.376, B:R.376, B:R.376 pi-Stacking: E:F.343, E:F.343

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.179, D.272 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.179 MG.4: 3 residues within 4Å: Chain B: T.179, Q.211 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.179 MG.6: 3 residues within 4Å: Chain C: T.179, D.272 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.179 MG.8: 4 residues within 4Å: Chain E: T.167, R.193, E.196 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.167

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 8 residues within 4Å: Chain C: R.376 Chain F: A.162, G.163, V.164, G.165, K.166, T.167, R.193 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:G.163, F:V.164, F:G.165, F:K.166, F:T.167, F:T.167 Salt bridges: F:K.166, F:R.193, C:R.376

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.10: 16 residues within 4Å: Chain K: G.62, E.65, A.66, Y.68, F.69, L.72 Chain L: L.63, A.66, A.67, I.70, F.74 Chain T: L.170, P.172, I.173, V.176 Ligands: YGR.16 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:E.65, K:A.66, K:F.69, K:F.69, L:I.70 Salt bridges: K:E.65 YGR.11: 15 residues within 4Å: Chain N: G.62, E.65, A.66, Y.68, F.69, L.72 Chain O: L.63, A.67, I.70 Chain T: F.213, P.214, V.217, W.218, F.221 Ligands: YGR.12 5 PLIP interactions: 2 interactions with chain T, 2 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: T:F.221, N:E.65, O:I.70 pi-Stacking: T:F.221 Salt bridges: N:E.65 YGR.12: 13 residues within 4Å: Chain O: G.62, E.65, A.66, Y.68, F.69, L.72 Chain P: L.63, A.66, A.67, I.70, F.74 Ligands: YGR.11, YGR.13 6 PLIP interactions: 5 interactions with chain O, 1 interactions with chain P Hydrophobic interactions: O:E.65, O:A.66, O:F.69, O:L.72, P:I.70 Salt bridges: O:E.65 YGR.13: 11 residues within 4Å: Chain P: G.62, E.65, A.66, F.69, L.72 Chain Q: L.63, A.66, A.67, I.70 Ligands: YGR.12, YGR.14 5 PLIP interactions: 4 interactions with chain P, 1 interactions with chain Q Hydrophobic interactions: P:A.66, P:F.69, P:F.69, Q:I.70 Salt bridges: P:E.65 YGR.14: 12 residues within 4Å: Chain Q: G.62, E.65, A.66, Y.68, F.69, L.72 Chain R: L.63, A.66, A.67, I.70 Ligands: YGR.13, YGR.15 3 PLIP interactions: 3 interactions with chain Q Hydrophobic interactions: Q:E.65, Q:F.69 Salt bridges: Q:E.65 YGR.15: 11 residues within 4Å: Chain R: G.62, E.65, A.66, Y.68, F.69, L.72 Chain S: L.63, A.66, A.67, I.70 Ligands: YGR.14 6 PLIP interactions: 5 interactions with chain R, 1 interactions with chain S Hydrophobic interactions: R:E.65, R:A.66, R:F.69, R:F.69, S:I.70 Salt bridges: R:E.65 YGR.16: 12 residues within 4Å: Chain K: L.63, A.66, A.67, I.70, F.74 Chain S: G.62, E.65, A.66, Y.68, F.69, L.72 Ligands: YGR.10 5 PLIP interactions: 4 interactions with chain S, 1 interactions with chain K Hydrophobic interactions: S:E.65, S:A.66, S:F.69, K:I.70 Salt bridges: S: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 alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H
ATP synthase subunit b: I
ATP synthase subunit b-delta: J
ATP synthase subunit c: KLMNOPQRS
ATP synthase subunit a: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
b

J
d

K
9

L
1

M
2

N
3

O
4

P
5

Q
6

R
7

S
8

T
a

Membrane

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

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

ATP synthase subunit b

ATP synthase subunit b-delta

ATP synthase subunit c

ATP synthase subunit a

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