SMTL ID : 7xkq.1

F1 domain of FoF1-ATPase with the down form of epsilon subunit from Bacillus PS3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.349, R.354, Q.422, L.424 Chain D: Y.375 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.172, A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:T.176, A:S.177, A:S.177, A:Q.422 Salt bridges: A:K.175, A:K.175 pi-Stacking: A:F.349 ATP.4: 14 residues within 4Å: Chain B: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, Q.200, E.320, F.349, R.354, Q.422, L.424 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.172, B:Q.172, B:T.173, B:G.174, B:K.175, B:T.176, B:S.177, B:S.177, B:R.354, B:Q.422 Salt bridges: B:K.175, B:K.175 pi-Stacking: B:F.349 ATP.5: 16 residues within 4Å: Chain C: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, E.320, F.349, R.354, Q.422, D.423, L.424 Chain F: Y.375 Ligands: MG.6 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.172, C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:T.176, C:S.177, C:S.177, C:E.320, C:Q.422, F:Y.375 Salt bridges: C:K.175, C:K.175 ATP.9: 13 residues within 4Å: Chain A: R.365 Chain E: A.171, G.172, V.173, G.174, K.175, T.176, V.177, Y.352, F.425, A.428, F.431 Ligands: MG.10 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:G.172, E:V.173, E:G.174, E:K.175, E:T.176, E:T.176, E:V.177 pi-Stacking: E:Y.352, E:Y.352 Salt bridges: A:R.365 ATP.11: 17 residues within 4Å: Chain B: S.336, V.363, R.365 Chain F: G.172, V.173, G.174, K.175, T.176, V.177, E.201, R.202, E.205, Y.352, F.425, A.428, F.431 Ligands: MG.12 17 PLIP interactions: 13 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:G.170, F:G.172, F:V.173, F:G.174, F:G.174, F:K.175, F:T.176, F:V.177, B:S.336 Salt bridges: F:K.175, F:K.175, F:R.202, B:R.365, B:R.365, B:R.365 pi-Stacking: F:Y.352, F:Y.352 ATP.13: 12 residues within 4Å: Chain G: A.147, K.150 Chain H: A.81, E.83, I.88, D.89, R.92, A.93, R.99, R.115, R.122, R.126 15 PLIP interactions: 13 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:E.83, H:D.89, H:D.89, H:R.92 Salt bridges: H:R.92, H:R.92, H:R.99, H:R.115, H:R.122, H:R.122, H:R.126, H:R.126, G:K.150, G:K.150 pi-Cation interactions: H:R.126

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.176 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.176 MG.3: 2 residues within 4Å: Chain B: T.176 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: T.176 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.176 MG.7: 5 residues within 4Å: Chain D: T.176, E.201, R.202, E.205 Ligands: ADP.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.176, D:E.201 MG.10: 2 residues within 4Å: Chain E: T.176 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain F: T.176, E.201, R.202, E.205 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.176, F:E.201

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

ADP.8: 17 residues within 4Å: Chain C: V.363, S.364, R.365, R.383 Chain D: G.170, A.171, G.172, V.173, G.174, K.175, T.176, V.177, Y.352, F.425, A.428, F.431 Ligands: MG.7 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.170, D:G.172, D:V.173, D:G.174, D:K.175, D:T.176, D:V.177, D:E.205, C:R.383 Salt bridges: D:K.175, C:R.365, C:R.365 pi-Stacking: D:Y.352, D:Y.352, D:F.431

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakano, A. et al., Structural basis of unisite catalysis of bacterial F 0 F 1 -ATPase. Pnas Nexus (2022)

Release Date

2022-09-21

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

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