SMTL ID : 8hhb.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-mer

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: D.169, R.170, 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:G.173, A:K.174, A:T.175, A:T.175, A:S.176, A:S.176, A:E.319, A:Q.421 Salt bridges: A:K.174, A:K.174 ATP.3: 14 residues within 4Å: Chain B: R.170, Q.171, T.172, G.173, K.174, T.175, S.176, E.319, F.348, R.353, D.422, L.423 Chain E: E.368 Ligands: MG.4 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain E 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:L.423, E:R.363, E:E.368 Salt bridges: B:K.174, B:K.174 pi-Cation interactions: B:R.353 ATP.6: 14 residues within 4Å: Chain C: R.170, Q.171, T.172, G.173, K.174, T.175, S.176, F.348, R.353, P.354, Q.421, L.423 Chain F: Y.375 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Q.171, C:Q.171, C:T.172, C:G.173, C:K.174, C:T.175, C:S.176, C:E.319, C:Q.421 Salt bridges: C:K.174, C:K.174 pi-Cation interactions: C:R.353 ATP.10: 19 residues within 4Å: Chain B: I.334, S.335, V.362, R.364 Chain F: G.170, 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.11 16 PLIP interactions: 12 interactions with chain F, 4 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, B:S.335 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

5 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.4: 3 residues within 4Å: Chain B: T.175, Q.199 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.175 MG.5: 2 residues within 4Å: Chain C: T.175 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.175 MG.7: 3 residues within 4Å: Chain D: T.176 Ligands: PO4.8, ADP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.176 MG.11: 5 residues within 4Å: Chain F: T.176, E.201, R.202, E.205 Ligands: ATP.10 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.176, F:E.201

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

PO4.8: 10 residues within 4Å: Chain C: R.364 Chain D: A.171, G.172, K.175, R.202, N.264, R.267, Y.318 Ligands: MG.7, ADP.9 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.170, D:G.172, D:T.176, D:N.264 Salt bridges: D:K.175, D:R.202, D:R.267, C:R.364

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

ADP.9: 15 residues within 4Å: Chain C: R.364 Chain D: G.170, G.172, V.173, G.174, K.175, T.176, V.177, E.205, Y.352, F.425, A.428, F.431 Ligands: MG.7, PO4.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.172, D:V.173, D:G.174, D:K.175, D:T.176, 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

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

2023-07-19

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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