SMTL ID : 7jga.1

Cryo-EM structure of bedaquiline-saturated Mycobacterium smegmatis ATP synthase rotational state 3

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-1-1-9-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, F.360, R.365, Q.433, P.434, Q.435 Chain F: S.353, D.357, Y.366 Ligands: MG.2 16 PLIP interactions: 2 interactions with chain F, 14 interactions with chain A Hydrogen bonds: F:S.353, F:D.357, A:K.175, A:T.176, A:G.177, A:K.178, A:T.179, A:A.180, A:Q.433, A:Q.435, A:Q.435 Salt bridges: A:K.175, A:K.175, A:K.175, A:K.178, A:K.178 ATP.3: 17 residues within 4Å: Chain B: R.174, K.175, T.176, G.177, K.178, T.179, A.180, Q.211, E.331, F.360, R.365, P.366, Q.433, Q.435 Chain D: T.354, D.357 Ligands: MG.4 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.175, B:T.176, B:G.177, B:K.178, B:T.179, B:T.179, B:A.180, B:Q.211, B:E.331, B:R.365, B:Q.433, B:Q.435, D:D.357 Salt bridges: B:K.175, B:K.178, B:K.178 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, Q.435 Chain E: D.357, Y.366 Ligands: MG.6 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:K.175, C:T.176, C:G.177, C:K.178, C:T.179, C:A.180, C:E.331, C:Q.433, C:Q.435, E:D.357 Salt bridges: C:K.175, C:K.178, C:K.178, C:K.178 pi-Stacking: C:F.360

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.179, Q.211, 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: 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, E.192, R.193 Ligands: ADP.7 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.167, E:E.192

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

ADP.7: 17 residues within 4Å: Chain B: V.374, R.376 Chain E: A.162, G.163, V.164, G.165, K.166, T.167, V.168, E.192, R.193, F.338, F.343, M.416, A.419, F.422 Ligands: MG.8 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:G.163, E:V.164, E:G.165, E:K.166, E:T.167, E:T.167, E:V.168, E:R.193 Salt bridges: E:K.166, E:R.193, B:R.376, B:R.376 pi-Stacking: E:F.343, E:F.343

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 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain F Salt bridges: C:R.376, F:K.166, F:R.193 Hydrogen bonds: F:G.163, F:G.165, F:K.166, F:T.167

7 x BQ1: Bedaquiline(Non-covalent)

BQ1.10: 14 residues within 4Å: Chain I: P.172, I.173, V.176 Chain L: A.28, G.62, E.65, A.66, Y.68, F.69, L.72 Chain M: L.63, A.66, A.67 Ligands: BQ1.16 8 PLIP interactions: 3 interactions with chain I, 5 interactions with chain L Hydrophobic interactions: I:P.172, I:P.172, I:V.176, L:F.69, L:F.69, L:L.72 Salt bridges: L:D.32, L:E.65 BQ1.11: 11 residues within 4Å: Chain I: F.213, V.217, F.221 Chain O: G.62, E.65, A.66, Y.68, F.69 Chain P: L.63, A.66, I.70 7 PLIP interactions: 3 interactions with chain I, 3 interactions with chain O, 1 interactions with chain P Hydrophobic interactions: I:F.213, I:V.217, I:F.221, O:E.65, O:F.69, P:I.70 Salt bridges: O:E.65 BQ1.12: 9 residues within 4Å: Chain P: G.62, E.65, A.66, Y.68, F.69 Chain Q: L.63, A.67, I.70 Ligands: BQ1.13 3 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain P Hydrophobic interactions: Q:I.70 Hydrogen bonds: P:E.65 Salt bridges: P:E.65 BQ1.13: 8 residues within 4Å: Chain Q: G.62, E.65, A.66, Y.68 Chain R: A.66, A.67, I.70 Ligands: BQ1.12 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain R Hydrophobic interactions: Q:A.66, R:I.70 Salt bridges: Q:E.65 BQ1.14: 8 residues within 4Å: Chain R: G.62, E.65, A.66, Y.68, F.69 Chain S: A.66, A.67, I.70 6 PLIP interactions: 6 interactions with chain R Hydrophobic interactions: R:E.65, R:F.69, R:F.69 Hydrogen bonds: R:E.65 Salt bridges: R:E.65 pi-Stacking: R:F.69 BQ1.15: 9 residues within 4Å: Chain S: G.62, E.65, A.66, Y.68, F.69 Chain T: A.66, A.67, I.70 Ligands: BQ1.16 5 PLIP interactions: 1 interactions with chain T, 4 interactions with chain S Hydrophobic interactions: T:I.70, S:F.69, S:F.69 Hydrogen bonds: S:E.65 Salt bridges: S:E.65 BQ1.16: 11 residues within 4Å: Chain L: L.63, A.66, A.67, I.70 Chain T: G.62, E.65, A.66, Y.68, F.69 Ligands: BQ1.10, BQ1.15 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain L Hydrophobic interactions: T:A.66, T:F.69, L:I.70 Salt bridges: T:E.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, H. et al., Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline. Nature (2021)

Release Date

2020-08-19

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H
ATP synthase subunit a: I
ATP synthase subunit b: J
ATP synthase subunit b-delta: K
ATP synthase subunit c: LMNOPQRST

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
a

J
b

K
d

L
1

M
2

N
3

O
4

P
5

Q
6

R
7

S
8

T
9

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 a

ATP synthase subunit b

ATP synthase subunit b-delta

ATP synthase subunit c

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