SMTL ID : 8j0s.1

Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with bedaquiline(BDQ)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 15 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, P.434, Q.435 Chain E: Y.377 Ligands: MG.2 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:K.175, B:T.176, B:G.177, B:K.178, B:T.179, B:A.180, B:Q.433, B:Q.435, E:D.368, E:Y.377 Salt bridges: B:K.175, B:K.178, B:K.178 pi-Stacking: B:F.360 ATP.3: 15 residues within 4Å: Chain C: R.174, 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 F: D.368 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.175, C:T.176, C:T.176, C:G.177, C:K.178, C:T.179, C:A.180, C:R.365, C:Q.433 Salt bridges: C:K.175, C:K.178, C:K.178 ATP.5: 14 residues within 4Å: Chain D: R.174, K.175, T.176, G.177, K.178, T.179, A.180, F.360, R.365, Q.433, P.434, Q.435 Chain G: Y.377 Ligands: MG.6 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:K.175, D:T.176, D:T.176, D:G.177, D:K.178, D:T.179, D:A.180, D:Q.433, D:Q.435, G:Y.377 Salt bridges: D:K.175, D:K.178, D:K.178 pi-Stacking: D:F.360

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: T.179 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.179 MG.4: 4 residues within 4Å: Chain C: T.179, Q.211, D.272 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.179 MG.6: 2 residues within 4Å: Chain D: T.179 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.179 MG.8: 4 residues within 4Å: Chain E: T.178, E.203, R.204 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.178 MG.10: 5 residues within 4Å: Chain G: T.178, E.203, R.204, E.207 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.178

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.7: 16 residues within 4Å: Chain D: V.374, S.375, R.376 Chain E: G.174, V.175, G.176, K.177, T.178, V.179, F.349, F.354, M.427, A.430, F.433, T.434 Ligands: MG.8 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:G.174, E:V.175, E:G.176, E:G.176, E:K.177, E:T.178, E:V.179, D:S.375 Salt bridges: E:K.177, D:R.376, D:R.376 pi-Stacking: E:F.354, E:F.354 ADP.9: 18 residues within 4Å: Chain C: V.374, R.376 Chain G: G.172, A.173, G.174, V.175, G.176, K.177, T.178, V.179, R.204, E.207, F.349, F.354, M.427, A.430, F.433 Ligands: MG.10 14 PLIP interactions: 13 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:G.172, G:G.172, G:G.174, G:V.175, G:G.176, G:K.177, G:T.178, G:T.178, G:V.179, G:R.204 Salt bridges: G:K.177, C:R.376 pi-Stacking: G:F.354, G:F.354

7 x BQ1: Bedaquiline(Non-covalent)

BQ1.11: 12 residues within 4Å: Chain A: L.168, P.170, I.171, V.174 Chain J: E.61, A.62, Y.64, F.65, L.68 Chain K: A.62, A.63, I.66 9 PLIP interactions: 2 interactions with chain A, 6 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: A:P.170, A:V.174, J:E.61, J:F.65, J:F.65, J:F.65, J:L.68, K:I.66 Salt bridges: J:E.61 BQ1.12: 11 residues within 4Å: Chain A: I.215, W.216, F.219 Chain M: E.61, A.62, Y.64, F.65, L.68 Chain N: A.62, A.63, I.66 11 PLIP interactions: 4 interactions with chain A, 6 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: A:I.215, A:I.215, A:F.219, A:F.219, M:E.61, M:F.65, M:F.65, M:F.65, M:L.68, N:I.66 Salt bridges: M:E.61 BQ1.13: 8 residues within 4Å: Chain N: G.58, E.61, A.62, Y.64, F.65 Chain O: A.62, A.63, I.66 5 PLIP interactions: 1 interactions with chain O, 4 interactions with chain N Hydrophobic interactions: O:I.66, N:E.61, N:F.65, N:F.65 Salt bridges: N:E.61 BQ1.14: 8 residues within 4Å: Chain O: G.58, E.61, A.62, Y.64, F.65 Chain P: A.62, A.63, I.66 5 PLIP interactions: 4 interactions with chain O, 1 interactions with chain P Hydrophobic interactions: O:E.61, O:F.65, O:F.65, P:I.66 Salt bridges: O:E.61 BQ1.15: 9 residues within 4Å: Chain P: G.58, E.61, A.62, Y.64, F.65, L.68 Chain Q: A.62, A.63, I.66 4 PLIP interactions: 1 interactions with chain Q, 3 interactions with chain P Hydrophobic interactions: Q:I.66, P:F.65, P:L.68 Salt bridges: P:E.61 BQ1.16: 8 residues within 4Å: Chain Q: E.61, A.62, Y.64, F.65 Chain R: A.62, A.63, I.66 Ligands: BQ1.17 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain R Hydrophobic interactions: Q:F.65, Q:F.65, R:I.66 Salt bridges: Q:E.61 BQ1.17: 10 residues within 4Å: Chain J: A.62, A.63, I.66 Chain R: G.58, E.61, A.62, Y.64, F.65, L.68 Ligands: BQ1.16 7 PLIP interactions: 6 interactions with chain R, 1 interactions with chain J Hydrophobic interactions: R:A.62, R:F.65, R:F.65, R:F.65, R:L.68, J:I.66 Salt bridges: R:E.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Inhibition of M. tuberculosis and human ATP synthase by BDQ and TBAJ-587. Nature (2024)

Release Date

2024-05-22

Peptides

ATP synthase subunit a: A
ATP synthase subunit alpha: BCD
ATP synthase subunit beta: EFG
ATP synthase gamma chain: H
ATP synthase epsilon chain: I
ATP synthase subunit c: JKLMNOPQR
ATP synthase subunit b: S
Multifunctional fusion protein: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
A

C
B

D
C

E
D

F
E

G
F

H
G

I
H

J
1

K
2

L
3

M
4

N
5

O
6

P
7

Q
8

R
9

S
b

T
d

Membrane

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

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

ATP synthase subunit c

ATP synthase subunit b

Multifunctional fusion protein

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