SMTL ID : 8hh3.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-mer

Ligands

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

ATP.1: 13 residues within 4Å: Chain A: Q.171, T.172, G.173, K.174, T.175, S.176, Q.199, E.319, R.353, P.354, L.423 Chain D: R.363 Ligands: MG.2 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain D Hydrogen bonds: 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:S.176, A:Q.199, D:R.363 Salt bridges: A:K.174, A:K.174 ATP.4: 13 residues within 4Å: Chain B: D.169, 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 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.171, B:T.172, B:G.173, B:K.174, B:T.175, B:T.175, B:Q.421 Salt bridges: B:K.174, B:K.174 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, L.423 Chain F: S.362, R.363 Ligands: MG.5 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Q.171, C:T.172, C:T.172, C:G.173, C:K.174, C:T.175, C:T.175, C:S.176, C:R.353, F:S.362, F:R.363 Salt bridges: C:K.174, C:K.174 ATP.11: 12 residues within 4Å: Chain E: G.170, G.172, V.173, G.174, K.175, T.176, V.177, Y.352, F.425, A.428, F.431, T.432 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.170, E:G.172, E:V.173, E:G.174, E:T.176, E:T.176, E:T.176, E:V.177, E:Y.352 pi-Stacking: E:Y.352, E:Y.352 ATP.13: 16 residues within 4Å: Chain B: S.335, V.362, R.364 Chain F: G.170, G.172, V.173, G.174, K.175, T.176, V.177, R.202, Y.352, F.425, A.428, F.431 Ligands: MG.12 19 PLIP interactions: 14 interactions with chain F, 5 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, F:Y.352, B:S.335, 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)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: T.175 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) 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.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: 4 residues within 4Å: Chain D: T.176, R.202 Ligands: PO4.8, ADP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.176 MG.12: 4 residues within 4Å: Chain B: R.364 Chain F: T.176, R.202 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.176

2 x PO4: PHOSPHATE ION(Non-covalent)

PO4.8: 7 residues within 4Å: Chain D: A.171, G.172, K.175, R.202, Y.318 Ligands: MG.7, ADP.9 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.171 Salt bridges: D:R.202 PO4.10: 3 residues within 4Å: Chain E: E.201, R.202, N.264 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.201, E:R.202 Salt bridges: E:K.175

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

ADP.9: 14 residues within 4Å: Chain C: S.363, R.364 Chain D: G.172, V.173, G.174, K.175, T.176, V.177, R.202, Y.352, P.353, T.432 Ligands: MG.7, PO4.8 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:S.363, D:G.174, D:K.175, D:T.176, D:V.177 Salt bridges: C:R.364, D:R.202 pi-Stacking: D:Y.352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakano, A. et al., Mechanism of ATP hydrolysis dependent rotation of bacterial ATP synthase. Nat Commun (2023)

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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