SMTL ID : 8hh6.1

F1 domain of FoF1-ATPase from Bacillus PS3,step waiting,highATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-mer

Ligands

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

ATP.1: 12 residues within 4Å: Chain A: Q.171, T.172, G.173, K.174, T.175, S.176, E.319, F.348, R.353, Q.421, L.423 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.169, A:Q.171, A:Q.171, A:T.172, A:T.172, A:G.173, A:K.174, A:T.175, A:T.175, A:S.176, A:S.176, A:Q.421 Salt bridges: A:K.174, A:K.174 ATP.4: 13 residues within 4Å: Chain B: R.170, Q.171, T.172, G.173, K.174, T.175, S.176, F.348, R.353, Q.421, D.422, L.423 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.171, B:Q.171, B:T.172, B:G.173, B:K.174, B:T.175, B:S.176, B:S.176, B:Q.421, B:L.423 Salt bridges: B:K.174, B:K.174 ATP.5: 16 residues within 4Å: Chain C: D.169, R.170, Q.171, T.172, G.173, K.174, T.175, S.176, F.348, R.353, Q.421, D.422, L.423 Chain F: R.363, Y.375 Ligands: MG.6 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:Q.171, C:Q.171, C:T.172, C:G.173, C:K.174, C:T.175, C:S.176, C:S.176, C:Q.421, F:R.363, F:Y.375, F:R.379 Salt bridges: C:K.174, C:K.174, F:R.363 pi-Stacking: C:F.348 ATP.10: 13 residues within 4Å: Chain E: G.170, A.171, G.172, V.173, G.174, K.175, T.176, V.177, E.205, Y.352, F.425, F.431 Ligands: MG.11 13 PLIP interactions: 13 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, E:E.205, E:E.205, E:Y.352 Salt bridges: E:K.175, E:K.175 pi-Stacking: E:Y.352 ATP.13: 21 residues within 4Å: Chain B: S.335, V.362, S.363, R.364 Chain F: G.170, A.171, G.172, V.173, G.174, K.175, T.176, V.177, E.201, R.202, Y.318, Y.352, P.353, F.425, A.428, F.431 Ligands: MG.12 17 PLIP interactions: 12 interactions with chain F, 5 interactions with chain B Hydrogen bonds: F:G.172, F:V.173, F:G.174, F:G.174, F:K.175, F:T.176, F:V.177, B:S.335, B:S.363 Salt bridges: F:K.175, F:K.175, F:R.202, B:R.364, B:R.364, B:R.364 pi-Stacking: F:Y.352, F:Y.352

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.175, Q.199, D.260 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.175 MG.3: 2 residues within 4Å: Chain B: T.175 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.175 MG.6: 2 residues within 4Å: Chain C: T.175 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.175 MG.7: 4 residues within 4Å: Chain D: T.176, E.205 Ligands: ADP.8, PO4.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.176 MG.11: 2 residues within 4Å: Chain E: T.176 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.176 MG.12: 3 residues within 4Å: Chain F: T.176, E.201 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.176

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

ADP.8: 14 residues within 4Å: Chain C: R.364 Chain D: G.170, A.171, G.172, V.173, G.174, K.175, T.176, V.177, Y.352, A.428, F.431 Ligands: MG.7, PO4.9 13 PLIP interactions: 11 interactions with chain D, 2 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:T.176, D:V.177, C:R.364 Salt bridges: D:K.175, C:R.364 pi-Stacking: D:Y.352, D:Y.352

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

PO4.9: 8 residues within 4Å: Chain C: R.364 Chain D: A.171, K.175, R.202, N.264, R.267 Ligands: MG.7, ADP.8 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.264 Salt bridges: D:K.175, D:R.202, D:R.267, C:R.364

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakano, A. et al., Rotation mechanism of ATP synthases driven by ATP hydrolysis. To Be Published

Release Date

2023-07-26

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

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