SMTL ID : 8g08.1

Cryo-EM structure of SQ31f-bound Mycobacterium smegmatis ATP synthase rotational state 1 (backbone model)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SQC.1: 2 residues within 4Å: Chain B: F.58 Chain M: G.62 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:A.67

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

ATP.2: 12 residues within 4Å: Chain C: R.174, K.175, T.176, G.177, K.178, T.179, A.180, R.365, P.366, Q.433, Q.435 Ligands: MG.3 8 PLIP interactions: 8 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, C:Q.435 ATP.4: 13 residues within 4Å: Chain D: D.173, R.174, K.175, T.176, G.177, K.178, T.179, A.180, R.365, Q.433, Q.435 Chain F: T.354 Ligands: MG.5 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:K.175, D:T.176, D:G.177, D:K.178, D:T.179, D:A.180, D:Q.433, D:Q.435, F:T.354 ATP.6: 12 residues within 4Å: Chain E: D.173, K.175, T.176, G.177, K.178, T.179, A.180, R.365, P.366, Q.433, Q.435 Ligands: MG.7 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:K.175, E:T.176, E:G.177, E:K.178, E:T.179, E:A.180, E:Q.433, E:Q.435 ATP.8: 11 residues within 4Å: Chain D: I.346, S.347 Chain G: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168 Ligands: MG.9 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:G.161, G:G.163, G:V.164, G:G.165, G:G.165, G:K.166, G:T.167, G:V.168

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 1 residues within 4Å: Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain D: T.179 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain E: T.179 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: ATP.8 No protein-ligand interaction detected (PLIP)

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

PO4.10: 5 residues within 4Å: Chain H: G.163, V.164, G.165, K.166, T.167 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:G.161, H:G.163, H:V.164, H:G.165, H:K.166, H:T.167

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 c: ABMNOPQRS
ATP synthase subunit alpha: CDE
ATP synthase subunit beta: FGH
ATP synthase gamma chain: I
ATP synthase epsilon chain: J
ATP synthase subunit b: K
ATP synthase subunit b-delta: L
ATP synthase subunit a: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
9

B
7

M
8

N
1

O
2

P
3

Q
4

R
5

S
6

C
B

D
C

E
A

F
E

G
F

H
D

I
G

J
H

K
b

L
d

T
a

Membrane

We predict this structure to be a membrane protein.
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ATP synthase subunit c

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 a

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