SMTL ID : 7xkr.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, E.320, F.349, R.354, Q.422, L.424 Chain D: R.363 Ligands: MG.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:S.177, A:S.177, A:R.354, A:Q.422, D:R.363 Salt bridges: A:K.175 ATP.3: 13 residues within 4Å: Chain B: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, E.320, F.349, R.354, Q.422, L.424 Ligands: MG.4 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain E Hydrogen bonds: 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, B:L.424, E:R.363 Salt bridges: B:K.175, B:K.175 pi-Stacking: B:F.349 ATP.6: 15 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, L.424 Chain F: Y.375 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Q.172, C:Q.172, C:T.173, C:T.173, C:G.174, C:K.175, C:T.176, C:S.177, C:S.177, C:E.320, C:Q.422 Salt bridges: C:K.175, C:K.175 ATP.9: 13 residues within 4Å: Chain E: 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.8 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.172, E:V.173, E:G.174, E:K.175, E:T.176, E:T.176, E:V.177 Salt bridges: E:K.175 pi-Stacking: E:Y.352, E:Y.352

5 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.4: 2 residues within 4Å: Chain B: T.176 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.176 MG.5: 2 residues within 4Å: Chain C: T.176 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.176 MG.8: 2 residues within 4Å: Chain E: T.176 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.176 MG.10: 4 residues within 4Å: Chain F: T.176, E.201, R.202 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.176

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

ADP.7: 12 residues within 4Å: 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 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.172, D:V.173, D:G.174, D:K.175, D:T.176, D:T.176, D:V.177 pi-Stacking: D:Y.352, D:Y.352 ADP.11: 14 residues within 4Å: Chain B: V.363, R.365 Chain F: G.170, G.172, V.173, G.174, K.175, T.176, V.177, Y.352, F.425, A.428, F.431 Ligands: MG.10 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:G.172, F:V.173, F:G.174, F:K.175, F:T.176, F:T.176, F:V.177, F:R.202, B:R.365 Salt bridges: F:K.175, B:R.365, B:R.365 pi-Stacking: F:Y.352, F:Y.352

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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