SMTL ID : 7y5c.1

Cryo-EM structure of F-ATP synthase from Mycolicibacterium smegmatis (rotational state 2)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.179 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain B: T.179 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain C: T.179 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.179 MG.7: 5 residues within 4Å: Chain D: G.171, K.172, T.173, V.174 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.173 MG.10: 2 residues within 4Å: Chain F: T.173 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.173

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

ATP.2: 13 residues within 4Å: Chain A: R.174, K.175, T.176, G.177, K.178, T.179, F.360, R.365, Q.433, P.434, Q.435 Chain F: Y.372 Ligands: MG.1 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:T.176, A:G.177, A:K.178, A:T.179, A:T.179, A:A.180, A:Q.433, A:Q.435, A:Q.435, F:D.363, F:Y.372 Salt bridges: A:K.178, A:K.178 ATP.4: 12 residues within 4Å: Chain B: K.175, T.176, G.177, K.178, T.179, A.180, F.360, R.365, Q.433, P.434, Q.435 Ligands: MG.3 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.176, B:G.177, B:K.178, B:T.179, B:T.179, B:A.180, B:Q.211, B:Q.433, B:Q.435, B:Q.435 Salt bridges: B:K.175, B:K.175, B:K.178 pi-Stacking: B:F.360 ATP.6: 13 residues within 4Å: Chain C: K.175, T.176, G.177, K.178, T.179, E.331, F.360, R.365, Q.433, P.434, Q.435 Chain E: D.363 Ligands: MG.5 14 PLIP interactions: 13 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:T.179, C:E.331, C:Q.433, C:Q.435, E:D.363 Salt bridges: C:K.175, C:K.175, C:K.175, C:K.178 ATP.8: 15 residues within 4Å: Chain A: V.374, S.375, R.376 Chain D: A.168, G.169, V.170, G.171, K.172, T.173, V.174, R.199, F.349, A.425, F.428 Ligands: MG.7 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:G.169, D:V.170, D:G.171, D:K.172, D:T.173, D:T.173, D:V.174, A:S.375 Salt bridges: D:K.172, D:K.172, D:R.199, A:R.376, A:R.376, A:R.376 pi-Stacking: D:F.349 ATP.11: 13 residues within 4Å: Chain C: V.374, R.376 Chain F: G.169, V.170, G.171, K.172, T.173, V.174, F.349, M.422, A.425, F.428 Ligands: MG.10 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:G.169, F:V.170, F:G.171, F:K.172, F:T.173, F:V.174, C:R.376 Salt bridges: F:R.199, C:R.376

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

ADP.9: 11 residues within 4Å: Chain E: G.167, A.168, G.169, V.170, G.171, K.172, T.173, V.174, F.344, I.348, F.349 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.167, E:G.169, E:V.170, E:G.171, E:K.172, E:T.173, E:V.174, E:F.349 pi-Stacking: E:F.344

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wong, C.F. et al., Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors. Antimicrob.Agents Chemother. (2022)

Release Date

2022-11-23

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
7

M
8

N
9

O
1

P
2

Q
3

R
4

S
5

T
6

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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