SMTL ID : 8ki3.1

Structure of the human ATP synthase bound to bedaquiline (composite)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-8-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, G.431, Q.432 Chain D: S.358, R.359, Y.371 Ligands: MG.2 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:S.177, A:S.177, A:Q.430, A:Q.432, D:S.358, D:R.359 Salt bridges: A:K.175, A:K.175 pi-Stacking: A:F.357 ATP.3: 16 residues within 4Å: Chain B: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, G.431, Q.432 Chain E: R.359, D.362 Ligands: MG.4 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:Q.172, B:T.173, B:G.174, B:K.175, B:T.176, B:S.177, B:S.177, B:R.362, B:Q.430, B:Q.432, E:R.359 Salt bridges: B:K.175, B:K.175, E:R.359 pi-Stacking: B:F.357 ATP.5: 17 residues within 4Å: Chain C: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, G.431, Q.432 Chain F: S.358, R.359, Y.371 Ligands: MG.6 16 PLIP interactions: 3 interactions with chain F, 13 interactions with chain C Hydrogen bonds: F:S.358, F:R.359, F:Y.371, C:Q.172, C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:T.176, C:S.177, C:S.177, C:Q.430, C:Q.432 Salt bridges: C:K.175, C:K.175

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.176 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.176 MG.4: 4 residues within 4Å: Chain B: T.176, Q.208, D.269 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.176 MG.6: 2 residues within 4Å: Chain C: T.176 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.176 MG.8: 4 residues within 4Å: Chain D: T.166, E.191, D.259 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.166 MG.10: 4 residues within 4Å: Chain F: T.166, E.191, R.192 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.166

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

ADP.7: 16 residues within 4Å: Chain C: R.373 Chain D: G.160, A.161, G.162, V.163, G.164, K.165, T.166, V.167, E.195, Y.348, F.421, A.424, F.427, T.428 Ligands: MG.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.160, D:G.162, D:V.163, D:G.164, D:K.165, D:T.166, D:T.166, D:V.167 Salt bridges: D:K.165, C:R.373, C:R.373 pi-Stacking: D:Y.348, D:Y.348 ADP.9: 13 residues within 4Å: Chain B: V.371, R.373 Chain F: G.160, G.162, V.163, G.164, K.165, T.166, V.167, Y.348, F.421, F.427 Ligands: MG.10 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:G.160, F:G.162, F:V.163, F:G.164, F:K.165, F:T.166, F:V.167, F:R.192, B:R.373 Salt bridges: F:K.165, B:R.373, B:R.373 pi-Stacking: F:Y.348, F:Y.348

1 x BQ1: Bedaquiline(Non-covalent)

BQ1.11: 9 residues within 4Å: Chain M: V.18, E.58, G.61, L.62, L.65 Chain N: M.60, F.63 Chain V: I.192, I.195 10 PLIP interactions: 1 interactions with chain N, 3 interactions with chain V, 6 interactions with chain M Hydrophobic interactions: N:F.63, V:I.192, V:I.195, V:I.195, M:E.58, M:E.58, M:L.62, M:L.65 Hydrogen bonds: M:E.58 Salt bridges: M:E.58

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, mitochondrial: ABC
ATP synthase subunit beta, mitochondrial: DEF
ATP synthase subunit gamma, mitochondrial: G
ATPase inhibitor, mitochondrial: H
ATP synthase subunit O, mitochondrial: I
ATP synthase F(0) complex subunit C1, mitochondrial: JKLMNOPQ
ATP synthase subunit delta, mitochondrial: R
ATP synthase subunit epsilon, mitochondrial: S
ATP synthase F(0) complex subunit B1, mitochondrial: T
ATP synthase subunit d, mitochondrial: U
ATP synthase subunit a: V
ATP synthase subunit ATP5MJ, mitochondrial: W
ATP synthase protein 8: X
ATP synthase subunit f, mitochondrial: Y
ATP synthase subunit g, mitochondrial: Z
ATP synthase subunit e, mitochondrial: 0
ATP synthase-coupling factor 6, mitochondrial: 1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
J

I
O

J
1

K
2

L
3

M
4

N
5

O
6

P
7

Q
8

R
H

S
I

T
K

U
M

V
N

W
P

X
Q

Y
R

Z
S

0
T

1
L

Membrane

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

ATP synthase subunit beta, mitochondrial

ATP synthase subunit gamma, mitochondrial

ATPase inhibitor, mitochondrial

ATP synthase subunit O, mitochondrial

ATP synthase F(0) complex subunit C1, mitochondrial

ATP synthase subunit delta, mitochondrial

ATP synthase subunit epsilon, mitochondrial

ATP synthase F(0) complex subunit B1, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase subunit a

ATP synthase subunit ATP5MJ, mitochondrial

ATP synthase protein 8

ATP synthase subunit f, mitochondrial

ATP synthase subunit g, mitochondrial

ATP synthase subunit e, mitochondrial

ATP synthase-coupling factor 6, mitochondrial

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