SMTL ID : 8jr0.1

Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with TBAJ-587

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: R.174, K.175, T.176, G.177, K.178, T.179, A.180, E.331, F.360, R.365, P.366, Q.433, P.434, Q.435 Chain D: Y.377 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.175, A:T.176, A:G.177, A:K.178, A:T.179, A:A.180, A:Q.433 Salt bridges: A:K.175, A:K.175, A:K.178, A:K.178 pi-Stacking: A:F.360 ATP.3: 15 residues within 4Å: Chain B: R.174, 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 E: D.368 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.175, B:T.176, B:G.177, B:K.178, B:T.179, B:A.180, B:R.365, B:Q.433 Salt bridges: B:K.175, B:K.178, B:K.178 pi-Stacking: B:F.360 ATP.5: 16 residues within 4Å: Chain C: R.174, K.175, T.176, G.177, K.178, T.179, A.180, E.331, F.360, R.365, P.366, Q.433, P.434, Q.435 Chain F: Y.377 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.175, C:T.176, C:G.177, C:K.178, C:T.179, C:A.180, C:Q.433 Salt bridges: C:K.175, C:K.178, C:K.178 pi-Stacking: C:F.360

5 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: 4 residues within 4Å: Chain B: T.179, Q.211, D.272 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.179 MG.6: 2 residues within 4Å: Chain C: T.179 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.179 MG.8: 4 residues within 4Å: Chain D: T.178, E.203, D.265 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.178 MG.10: 4 residues within 4Å: Chain F: T.178, E.203, R.204 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.178

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

ADP.7: 16 residues within 4Å: Chain C: V.374, S.375, R.376 Chain D: A.173, G.174, V.175, G.176, K.177, T.178, V.179, F.349, F.354, M.427, A.430, F.433 Ligands: MG.8 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.174, D:V.175, D:G.176, D:K.177, D:T.178, D:T.178, D:V.179, C:S.375 Salt bridges: D:K.177, C:R.376, C:R.376 pi-Stacking: D:F.354, D:F.354 ADP.9: 14 residues within 4Å: Chain B: V.374, R.376 Chain F: G.174, V.175, G.176, K.177, T.178, V.179, F.349, F.354, M.427, A.430, F.433 Ligands: MG.10 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.174, F:V.175, F:G.176, F:K.177, F:T.178, F:T.178, F:V.179, B:R.376 Salt bridges: F:K.177, B:R.376 pi-Stacking: F:F.354, F:F.354

7 x UTI: (1~{S},2~{S})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2-fluoranyl-3-methoxy-phenyl)butan-2-ol(Non-covalent)

UTI.11: 12 residues within 4Å: Chain I: E.61, A.62, Y.64, F.65, L.68 Chain J: A.62, A.63, I.66 Chain R: L.168, P.170, I.171, V.174 7 PLIP interactions: 6 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:E.61, I:F.65, I:F.65, I:F.65, I:L.68, J:I.66 Salt bridges: I:E.61 UTI.12: 10 residues within 4Å: Chain L: E.61, Y.64, F.65, L.68 Chain M: L.59, A.62, A.63, I.66 Chain R: I.215 Ligands: UTI.13 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain L Hydrophobic interactions: M:I.66, L:E.61, L:F.65 Salt bridges: L:E.61 UTI.13: 9 residues within 4Å: Chain M: E.61, A.62, Y.64, F.65, L.68 Chain N: A.62, A.63, I.66 Ligands: UTI.12 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:E.61, M:F.65, M:L.68 Salt bridges: M:E.61 UTI.14: 10 residues within 4Å: Chain N: G.58, E.61, A.62, Y.64, F.65, L.68 Chain O: A.62, A.63, I.66 Ligands: UTI.15 2 PLIP interactions: 1 interactions with chain O, 1 interactions with chain N Hydrophobic interactions: O:I.66 Salt bridges: N:E.61 UTI.15: 9 residues within 4Å: Chain O: E.61, Y.64, F.65, L.68 Chain P: A.62, A.63, I.66 Ligands: UTI.14, UTI.16 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 UTI.16: 7 residues within 4Å: Chain P: E.61, F.65 Chain Q: L.59, A.62, A.63, I.66 Ligands: UTI.15 6 PLIP interactions: 1 interactions with chain Q, 5 interactions with chain P Hydrophobic interactions: Q:I.66, P:E.61, P:F.65, P:F.65, P:F.65 Salt bridges: P:E.61 UTI.17: 8 residues within 4Å: Chain I: A.62, A.63, I.66 Chain Q: E.61, A.62, Y.64, F.65, L.68 7 PLIP interactions: 1 interactions with chain I, 6 interactions with chain Q Hydrophobic interactions: I:I.66, Q:E.61, Q:F.65, Q:F.65, Q:F.65, Q:F.65 Salt bridges: Q: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

2024-05-01

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H
ATP synthase subunit c: IJKLMNOPQ
ATP synthase subunit a: R
ATP synthase subunit b: S
Multifunctional fusion protein: 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
1

J
2

K
3

L
4

M
5

N
6

O
7

P
8

Q
9

R
a

S
b

T
d

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 c

ATP synthase subunit a

ATP synthase subunit b

Multifunctional fusion protein

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