SMTL ID : 7l1q.1

PS3 F1-ATPase Binding/TS Dwell

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-mer

Ligands

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

ATP.1: 13 residues within 4Å: Chain A: R.179, Q.180, T.181, G.182, K.183, T.184, S.185, F.357, R.362, Q.430, D.431, L.432 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.179, A:Q.180, A:T.181, A:G.182, A:K.183, A:T.184, A:S.185, A:S.185, A:R.362, A:Q.430 Salt bridges: A:K.183 ATP.3: 11 residues within 4Å: Chain B: Q.180, T.181, G.182, K.183, T.184, S.185, R.362, P.363, Q.430, L.432 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.178, B:Q.180, B:T.181, B:G.182, B:K.183, B:T.184, B:S.185, B:S.185, B:Q.430, B:L.432 Salt bridges: B:K.183, B:K.183 ATP.6: 13 residues within 4Å: Chain C: Q.180, T.181, G.182, K.183, T.184, S.185, F.357, R.362, Q.430, D.431, L.432 Chain F: R.379 Ligands: MG.5 12 PLIP interactions: 1 interactions with chain F, 11 interactions with chain C Hydrogen bonds: F:R.379, C:Q.180, C:T.181, C:G.182, C:K.183, C:T.184, C:T.184, C:S.185, C:S.185, C:Q.430 Salt bridges: C:K.183, C:K.183 ATP.10: 13 residues within 4Å: Chain A: R.373 Chain E: A.171, G.172, V.173, G.174, K.175, T.176, V.177, R.202, E.205, Y.352, F.431 Ligands: MG.11 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain E Salt bridges: A:R.373, A:R.373, E:K.175, E:R.202 Hydrogen bonds: E:K.175, E:T.176, E:T.176, E:V.177 pi-Stacking: E:Y.352, E:Y.352 ATP.12: 14 residues within 4Å: Chain B: S.344, V.371, R.373 Chain F: G.172, V.173, G.174, K.175, T.176, V.177, R.202, Y.352, F.425, F.431 Ligands: MG.13 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.172, F:V.173, F:G.174, F:K.175, F:T.176, F:V.177 Salt bridges: F:K.175, F:R.202, B:R.373, B:R.373 pi-Stacking: F:Y.352, F:Y.352

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: K.183, T.184 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.184 MG.4: 2 residues within 4Å: Chain B: T.184 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.184 MG.5: 3 residues within 4Å: Chain C: T.184, Q.208 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain D: T.176, R.267 Ligands: ADP.7, PO4.8 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain E: T.176, E.205 Ligands: ATP.10 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.176, E:E.205 MG.13: 3 residues within 4Å: Chain F: T.176, D.263 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.176

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

ADP.7: 13 residues within 4Å: Chain C: R.373, G.375 Chain D: G.174, K.175, T.176, V.177, R.202, E.205, A.428, F.431, T.432 Ligands: PO4.8, MG.9 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:V.173, D:G.174, D:K.175, D:T.176, D:T.176, D:R.202, C:R.373 pi-Stacking: D:Y.352 Salt bridges: C:R.373

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

PO4.8: 7 residues within 4Å: Chain C: R.373 Chain D: K.175, R.202, N.264, R.267 Ligands: ADP.7, MG.9 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.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sobti, M. et al., The six steps of the complete F 1 -ATPase rotary catalytic cycle. Nat Commun (2021)

Release Date

2021-07-21

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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