SMTL ID : 8hh9.1

F1 domain of FoF1-ATPase from Bacillus PS3, 90 degrees, low ATP

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: 13 residues within 4Å: Chain A: 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.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.171, A:T.172, A:G.173, A:K.174, A:T.175, A:T.175, A:S.176, A:D.422 Salt bridges: A:R.170, A:K.174, A:K.174 ATP.3: 15 residues within 4Å: Chain B: D.169, R.170, Q.171, T.172, G.173, K.174, T.175, S.176, F.348, R.353, P.354, Q.421 Chain E: R.363, E.368 Ligands: MG.4 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Q.171, B:T.172, B:G.173, B:K.174, B:T.175, B:S.176, B:S.176, B:E.319, B:Q.421, E:R.363 Salt bridges: B:K.174 ATP.6: 15 residues within 4Å: Chain C: D.169, R.170, Q.171, T.172, G.173, K.174, T.175, S.176, E.319, F.348, R.353, Q.421, D.422, L.423 Ligands: MG.5 13 PLIP interactions: 13 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:S.176, C:E.319, C:Q.421 Salt bridges: C:K.174, C:K.174 pi-Cation interactions: C:R.353 ATP.11: 18 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, A.428, F.431 Ligands: MG.12 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, B:R.364 Salt bridges: F:K.175, F:K.175, F:R.202, B:R.364, B:R.364 pi-Stacking: F:Y.352, F:Y.352

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.175 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) 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: 2 residues within 4Å: Chain D: T.176 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.176 MG.12: 5 residues within 4Å: Chain F: T.176, E.201, R.202, E.205 Ligands: ATP.11 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.176, F:E.201, F:E.205

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

PO4.8: 10 residues within 4Å: Chain C: I.334, S.335, R.364 Chain D: G.170, A.171, G.172, R.202, R.267, Y.318 Ligands: ADP.9 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.172, D:R.267, D:Y.318, D:Y.318, C:I.334 Salt bridges: D:K.175, D:R.202, C:R.364 PO4.10: 6 residues within 4Å: Chain E: G.169, K.175, D.263, N.264, A.316, I.317 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.169, E:N.264 Salt bridges: E:K.175

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

ADP.9: 15 residues within 4Å: Chain C: S.363, R.364 Chain D: 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, PO4.8 13 PLIP interactions: 10 interactions with chain D, 3 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:V.177, C:S.363 Salt bridges: D:K.175, C:R.364, 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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