SMTL ID : 6yy0.1

bovine ATP synthase F1-peripheral stalk domain, state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-1-1-1-1-1-mer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, G.431, Q.432 Chain D: R.360, D.363, Y.372, R.376 Ligands: MG.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.172, A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:T.176, A:S.177, A:S.177, A:Q.430, A:Q.432, D:D.363 Water bridges: A:T.176 Salt bridges: A:K.175, A:K.175 pi-Stacking: A:F.357 ATP.3: 18 residues within 4Å: Chain B: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, E.328, F.357, R.362, P.363, Q.430, G.431, Q.432 Chain E: R.360, D.363 Ligands: MG.4 18 PLIP interactions: 3 interactions with chain E, 15 interactions with chain B Hydrogen bonds: E:R.360, E:D.363, B:Q.172, B:Q.172, B:T.173, B:G.174, B:K.175, B:T.176, B:T.176, B:S.177, B:S.177, B:R.362, B:Q.430, B:Q.432 Salt bridges: E:R.360, B:K.175, B:K.175 Water bridges: B:T.176 ATP.5: 22 residues within 4Å: Chain C: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, E.328, F.357, R.362, P.363, Q.430, G.431, Q.432 Chain F: S.359, R.360, M.362, D.363, Y.372, R.376 Ligands: MG.6 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Q.172, C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:S.177, C:S.177, C:E.328, C:Q.430, C:Q.432, F:R.360, F:Y.372 Water bridges: C:T.176 Salt bridges: C:K.175, C:K.175 pi-Stacking: C:F.357

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.176 Ligands: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.176, H2O.1, H2O.1, H2O.1 MG.4: 2 residues within 4Å: Chain B: T.176 Ligands: ATP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.176, H2O.1, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain C: T.176 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.176, H2O.1, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain D: T.167, R.193, E.196 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.167, H2O.1, H2O.1, H2O.1, H2O.1 MG.11: 4 residues within 4Å: Chain F: T.167, R.193, E.196 Ligands: ADP.10 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.167, H2O.1, H2O.1, H2O.1, H2O.1

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

ADP.7: 19 residues within 4Å: Chain C: V.371, S.372, R.373 Chain D: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, R.193, Y.349, F.422, A.425, F.428, T.429, M.463 Ligands: MG.8 16 PLIP interactions: 3 interactions with chain C, 13 interactions with chain D Hydrogen bonds: C:S.372, D:G.161, D:G.163, D:V.164, D:G.165, D:K.166, D:T.167, D:T.167, D:V.168 Salt bridges: C:R.373, C:R.373, D:K.166 Water bridges: D:T.167, D:R.193 pi-Stacking: D:Y.349, D:Y.349 ADP.9: 16 residues within 4Å: Chain E: A.162, G.163, V.164, G.165, K.166, T.167, V.168, E.203, Y.349, P.350, Q.420, P.421, F.422, A.425, F.428, T.429 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.163, E:V.164, E:G.165, E:K.166, E:T.167, E:T.167, E:T.167, E:V.168 pi-Stacking: E:Y.349, E:Y.349 ADP.10: 21 residues within 4Å: Chain B: S.344, V.371, R.373 Chain F: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, R.193, Y.349, P.350, Q.420, F.422, A.425, F.428, T.429, M.463 Ligands: MG.11 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.163, F:V.164, F:G.165, F:K.166, F:T.167, F:V.168, B:R.373 Water bridges: F:T.167, F:T.167, F:R.193 Salt bridges: F:K.166, B:R.373 pi-Stacking: F:Y.349, F:Y.349, F:F.428

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spikes, T.E. et al., Structure of the dimeric ATP synthase from bovine mitochondria. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-09-09

Peptides

ATP synthase subunit alpha, mitochondrial: ABC
ATP synthase subunit beta, mitochondrial: DEF
ATP synthase subunit gamma, mitochondrial: G
ATP synthase subunit delta, mitochondrial: H
ATP synthase subunit epsilon, mitochondrial: I
ATPase inhibitor, mitochondrial: J
ATP synthase subunit O, mitochondrial: K
ATP synthase F(0) complex subunit B1, mitochondrial: L
ATP synthase subunit d, mitochondrial: M
ATP synthase-coupling factor 6, mitochondrial: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
S

L
b

M
d

N
h

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta, mitochondrial

ATP synthase subunit gamma, mitochondrial

ATP synthase subunit delta, mitochondrial

ATP synthase subunit epsilon, mitochondrial

ATPase inhibitor, mitochondrial

ATP synthase subunit O, mitochondrial

ATP synthase F(0) complex subunit B1, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase-coupling factor 6, mitochondrial

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