SMTL ID : 7tjx.1

Yeast ATP synthase F1 region State 1binding(a-d) with 10 mM 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.173, Q.174, T.175, G.176, K.177, T.178, A.179, R.364, Q.432, N.433, Q.434 Chain D: R.356 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.174, A:T.175, A:G.176, A:K.177, A:T.178, A:T.178, A:A.179, A:Q.432 Salt bridges: A:K.177, A:K.177 ATP.3: 13 residues within 4Å: Chain B: Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, Q.432, N.433, Q.434 Chain E: R.356 Ligands: MG.4 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:Q.174, B:T.175, B:G.176, B:K.177, B:T.178, B:A.179, B:Q.432, B:Q.434 Salt bridges: B:K.177, B:K.177, E:R.356, E:R.356, E:R.356 ATP.5: 18 residues within 4Å: Chain C: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, Q.210, F.359, R.364, P.365, Q.432, Q.434 Chain F: S.355, R.356, D.359, Y.368 Ligands: MG.6 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:G.176, C:K.177, C:T.178, C:A.179, C:Q.432, C:Q.434, F:S.355, F:D.359, F:Y.368 Salt bridges: C:K.177, C:K.177, F:R.356 pi-Stacking: C:F.359 ATP.10: 18 residues within 4Å: Chain B: I.345, S.346, V.373, R.375 Chain F: G.158, G.160, V.161, G.162, K.163, T.164, V.165, R.190, Y.345, F.418, A.421, F.424, T.425 Ligands: MG.11 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain F Hydrogen bonds: B:S.346, F:G.160, F:V.161, F:G.162, F:K.163, F:T.164, F:V.165 Salt bridges: B:R.375, B:R.375, B:R.375, F:R.190 pi-Stacking: F:Y.345, F:Y.345

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.178 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.178 MG.4: 2 residues within 4Å: Chain B: T.178 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.178 MG.6: 2 residues within 4Å: Chain C: T.178 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.178 MG.8: 6 residues within 4Å: Chain D: K.163, T.164, R.190, E.193 Ligands: ADP.7, PO4.9 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.164, D:E.193 MG.11: 3 residues within 4Å: Chain F: T.164, E.193 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.164

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

ADP.7: 15 residues within 4Å: Chain C: R.375 Chain D: A.159, G.160, V.161, G.162, K.163, T.164, V.165, Y.345, F.418, A.421, F.424, T.425 Ligands: MG.8, PO4.9 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.160, D:G.162, D:K.163, D:T.164, D:V.165, D:Y.345, C:R.375 Salt bridges: D:K.163, C:R.375 pi-Stacking: D:Y.345, D:Y.345

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

PO4.9: 9 residues within 4Å: Chain C: R.375 Chain D: K.163, T.164, R.190, E.193, N.257, R.260 Ligands: ADP.7, MG.8 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.257 Salt bridges: D:K.163, D:R.190, D:R.260, C:R.375

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, H. et al., Structure of ATP synthase under strain during catalysis. Nat Commun (2022)

Release Date

2022-04-20

Peptides

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

Related Entries With Identical Sequence