SMTL ID : 8g0a.1

Cryo-EM structure of SQ31f-bound Mycobacterium smegmatis ATP synthase rotational state 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: K.175, T.176, G.177, K.178, T.179, A.180, D.272, F.360, R.365, P.366, Q.433, Q.435 Chain F: Y.366 Ligands: MG.2 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain F Hydrogen bonds: 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, F:Y.366 Salt bridges: A:K.175, A:K.175, A:K.178, A:K.178 pi-Stacking: A:F.360 ATP.3: 14 residues within 4Å: Chain B: R.174, K.175, T.176, G.177, K.178, T.179, A.180, Q.211, F.360, R.365, Q.433, Q.435 Chain D: T.354 Ligands: MG.4 15 PLIP interactions: 14 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:E.331, B:Q.433, B:Q.435, B:Q.435, D:T.354 Salt bridges: B:K.175, B:K.178, B:K.178 pi-Stacking: B:F.360 ATP.5: 12 residues within 4Å: Chain C: K.175, T.176, G.177, K.178, T.179, A.180, F.360, R.365, Q.433, Q.435 Chain E: 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:T.176, C:G.177, C:K.178, C:T.179, C:A.180, C:Q.433, C:Q.435, C:Q.435, E:Y.366 Salt bridges: C:K.175, C:K.178, C:K.178 pi-Stacking: C:F.360 ATP.7: 21 residues within 4Å: Chain B: S.347, V.374, R.376 Chain E: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, E.192, R.193, E.196, F.338, F.343, M.416, A.419, F.422, T.423 Ligands: MG.8 16 PLIP interactions: 12 interactions with chain E, 4 interactions with chain B Hydrogen bonds: E:G.161, E:G.163, E:V.164, E:G.165, E:K.166, E:T.167, E:T.167, E:V.168, E:T.423, B:S.347 Salt bridges: E:K.166, E:K.166, E:R.193, B:R.376, B:R.376, B:R.376

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.179, Q.211, D.272 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.179, A:D.272 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: 5 residues within 4Å: Chain E: T.167, E.192, E.196, D.254 Ligands: ATP.7 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.167, E:E.192, E:D.254

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

PO4.9: 7 residues within 4Å: Chain C: R.376 Chain F: G.163, V.164, G.165, K.166, T.167, R.193 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:G.163, F:V.164, F:G.165, F:K.166, F:T.167 Salt bridges: F:K.166, F:R.193, C:R.376

1 x SQC: 3-[4-(morpholin-4-yl)phenyl]-4-{[(pyridin-2-yl)methyl]amino}cyclobut-3-ene-1,2-dione(Non-covalent)

SQC.10: 17 residues within 4Å: Chain K: G.62, L.63, A.66, I.70 Chain S: H.166, N.174, E.177, K.181, S.184, R.188, L.236, Y.240 Chain T: F.58, V.61, E.65, Y.68, F.69 13 PLIP interactions: 5 interactions with chain S, 3 interactions with chain K, 5 interactions with chain T Hydrophobic interactions: S:E.177, K:L.63, K:I.70, T:V.61, T:F.69, T:F.69 Hydrogen bonds: S:N.174, S:S.184, S:R.188, S:Y.240, K:A.67, T:E.65 pi-Stacking: T:Y.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Courbon, G.M. et al., Mechanism of mycobacterial ATP synthase inhibition by squaramides and second generation diarylquinolines. Embo J. (2023)

Release Date

2023-02-15

Peptides

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

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
b

J
d

K
2

L
3

M
4

N
5

O
6

P
7

Q
8

R
9

T
1

S
a

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 b

ATP synthase subunit b-delta

ATP synthase subunit c

ATP synthase subunit a

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