SMTL ID : 7jg5.1

Cryo-EM structure of bedaquiline-free Mycobacterium smegmatis ATP synthase rotational state 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-3-1-1-1-1-1-9-mer

Ligands

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

ATP.1: 13 residues within 4Å: Chain A: K.175, T.176, G.177, K.178, T.179, A.180, F.360, R.365, Q.433, Q.435 Chain F: T.354, Y.366 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.175, A:T.176, A:G.177, A:K.178, A:T.179, A:Q.433, A:Q.435, A:Q.435 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: 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 D: T.354, Y.366 Ligands: MG.4 11 PLIP interactions: 10 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:A.180, B:Q.433, B:Q.435, D:S.353 Salt bridges: B:K.178, B:K.178 ATP.5: 15 residues within 4Å: Chain C: K.175, T.176, G.177, K.178, T.179, A.180, Q.211, E.331, F.360, R.365, Q.433, P.434, Q.435 Chain E: D.357 Ligands: MG.6 14 PLIP interactions: 12 interactions with chain C, 2 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:R.365, C:Q.433, C:Q.435, E:D.357, E:D.357 Salt bridges: C:K.175, C:K.178, C:K.178

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: 2 residues within 4Å: Chain B: T.179 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.179 MG.6: 4 residues within 4Å: Chain C: T.179, Q.211, D.272 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.179 MG.10: 4 residues within 4Å: Chain F: K.166, T.167, R.193 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.167

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

PO4.7: 8 residues within 4Å: Chain A: R.376 Chain D: G.161, G.163, V.164, G.165, K.166, T.167, R.193 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.163, D:G.165, D:G.165, D:K.166, D:T.167, D:T.167 Salt bridges: D:K.166, D:R.193, A:R.376 PO4.8: 6 residues within 4Å: Chain E: K.166, T.167, I.170, F.187, E.196, D.254 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:K.166

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

ADP.9: 16 residues within 4Å: Chain C: S.347, V.374, R.376 Chain F: G.161, A.162, G.163, G.165, K.166, T.167, V.168, R.193, F.343, M.416, A.419, F.422 Ligands: MG.10 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:G.163, F:G.165, F:K.166, F:T.167, F:T.167, F:R.193, C:S.347 Salt bridges: F:K.166, F:R.193, C:R.376, C:R.376 pi-Stacking: F:F.343, F:F.343

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: AB
ATP synthase subunit alpha,ATP synthase subunit alpha: C
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 alpha,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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