SMTL ID : 6zqm.1

bovine ATP synthase monomer state 2 (combined)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-1-8-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: 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 D: T.358, S.359, R.360, D.363, Y.372, R.376 Ligands: MG.2 17 PLIP interactions: 16 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:K.175, A:K.175, A:T.176 Salt bridges: A:K.175, A:K.175 ATP.3: 17 residues within 4Å: Chain B: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, Q.208, F.357, R.362, P.363, Q.430, G.431, Q.432 Chain E: R.360, D.363 Ligands: MG.4 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain E Hydrogen bonds: 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, E:D.363 Water bridges: B:T.176, B:Q.208 Salt bridges: B:K.175, B:K.175, E:R.360, E:R.360 ATP.5: 20 residues within 4Å: Chain C: 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 F: S.359, R.360, M.362, D.363, Y.372, R.376 Ligands: MG.6 20 PLIP interactions: 16 interactions with chain C, 4 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:Q.430, C:Q.432, C:Q.432, F:R.360, F:R.360, F:Y.372 Water bridges: C:T.176, C:T.176 Salt bridges: C:K.175, C:K.175, F:R.360 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: 3 residues within 4Å: Chain B: T.176, Q.208 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: 3 residues within 4Å: Chain C: T.176, D.269 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: 5 residues within 4Å: Chain F: T.167, E.192, 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: 16 residues within 4Å: Chain C: V.371, R.373 Chain D: A.162, G.163, V.164, G.165, K.166, T.167, V.168, Y.349, P.350, F.422, A.425, F.428, T.429 Ligands: MG.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.163, D:V.164, D:G.165, D:K.166, D:T.167, D:T.167, D:V.168 Water bridges: D:R.193 Salt bridges: D:K.166, C:R.373, C:R.373 pi-Stacking: D:Y.349, D:Y.349 ADP.9: 15 residues within 4Å: Chain E: A.162, G.163, V.164, G.165, K.166, T.167, V.168, Y.349, P.350, Q.420, P.421, F.422, A.425, F.428, T.429 9 PLIP interactions: 9 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:V.168 pi-Stacking: E:Y.349, E:Y.349 ADP.10: 19 residues within 4Å: Chain B: V.371, R.373 Chain F: 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 16 PLIP interactions: 13 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:G.163, F:V.164, F:G.165, F:K.166, F:T.167, F:V.168, F:T.429 Water bridges: F:R.193, F:R.193, F:R.193, B:R.373 Salt bridges: F:K.166, B:R.373, B:R.373 pi-Stacking: F:Y.349, F:Y.349

3 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 33 residues within 4Å: Chain T: L.18, I.22, I.23, L.26, K.27, K.30 Chain U: L.19, L.22, I.23, L.25, F.26, S.28, L.29, P.32, T.33 Chain W: A.34, F.37, Q.38, G.40, Y.41, Y.42, A.65, Y.66, F.68, L.69 Chain Y: L.5, I.6, K.8, V.9, W.10, Y.17 Ligands: CDL.13, LHG.14 17 PLIP interactions: 6 interactions with chain U, 3 interactions with chain T, 5 interactions with chain W, 3 interactions with chain Y Hydrophobic interactions: U:L.22, U:I.23, U:L.25, U:F.26, U:L.29, T:I.22, T:I.23, W:Y.41, W:Y.41, Y:V.9 Hydrogen bonds: U:T.33, W:Q.38, W:Y.41, W:Y.42 Salt bridges: T:K.27, Y:K.8, Y:K.8 CDL.13: 35 residues within 4Å: Chain U: L.29, L.30, P.32 Chain W: L.12, G.40, Y.41, R.43, Y.44, Y.45, K.47, Y.48, V.49, G.58, L.59, M.61, V.62, A.64, A.65, V.67, F.68 Chain X: K.70, L.73, L.77 Chain Z: L.16, I.17, P.18, E.20, F.21, F.24, L.37, I.64 Ligands: CDL.12, LHG.14, CDL.15, LHG.16 14 PLIP interactions: 1 interactions with chain X, 11 interactions with chain W, 1 interactions with chain U, 1 interactions with chain Z Salt bridges: X:K.70, W:R.43, W:R.43, W:K.47 Hydrophobic interactions: W:Y.41, W:Y.41, W:Y.44, W:Y.44, W:Y.44, W:F.68, U:L.29, Z:F.21 Hydrogen bonds: W:R.43, W:R.43 CDL.15: 36 residues within 4Å: Chain U: L.30, F.31, R.41, F.42, L.45, Q.46, M.49, L.52, V.53, S.81, L.84, L.85, L.88, F.204, M.208 Chain W: G.54, S.55, I.56, L.59, S.60, L.63 Chain Z: F.14, G.15, L.16, I.64, F.66, L.67, V.68, I.70, V.71, K.72, G.75, A.76, V.78, G.79 Ligands: CDL.13 13 PLIP interactions: 4 interactions with chain U, 6 interactions with chain Z, 3 interactions with chain W Hydrophobic interactions: U:F.31, U:F.42, U:L.45, Z:F.14, Z:I.64, Z:L.67, Z:V.78, W:I.56, W:L.59 Hydrogen bonds: U:R.41, W:I.56 Salt bridges: Z:K.72, Z:K.72

2 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.14: 9 residues within 4Å: Chain W: K.10, L.11, L.12, R.39, R.43 Chain X: L.73 Ligands: CDL.12, CDL.13, LHG.16 7 PLIP interactions: 7 interactions with chain W Hydrogen bonds: W:R.39, W:R.39, W:R.43 Salt bridges: W:K.10, W:K.10, W:K.10, W:R.43 LHG.16: 20 residues within 4Å: Chain U: P.89, H.90 Chain W: V.67, F.68, Y.71, C.72, Y.75, K.79, R.82 Chain Z: G.38, L.41, I.42, Y.44, L.45, K.48, I.50, Y.51, A.60 Ligands: CDL.13, LHG.14 5 PLIP interactions: 3 interactions with chain W, 2 interactions with chain Z Hydrophobic interactions: W:F.68, W:Y.75 Salt bridges: W:K.79, Z:K.48, Z:K.48

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 F(0) complex subunit C2, mitochondrial: KLMNOPQR
ATP synthase subunit O, mitochondrial: S
ATP synthase protein 8: T
ATP synthase subunit a: U
ATP synthase subunit d, mitochondrial: V
ATP synthase subunit f, mitochondrial: W
ATP synthase subunit g, mitochondrial: X
ATP synthase subunit ATP5MPL, mitochondrial: Y
ATP synthase F(0) complex subunit B1, mitochondrial: Z
ATP synthase-coupling factor 6, mitochondrial: 0
ATP synthase membrane subunit DAPIT, mitochondrial: 1
ATP synthase subunit e, mitochondrial: 2

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
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
8

U
a

V
d

W
f

X
g

Y
j

Z
b

0
h

1
k

2
e

Membrane

We predict this structure to be a membrane protein.
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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 F(0) complex subunit C2, mitochondrial

ATP synthase subunit O, mitochondrial

ATP synthase protein 8

ATP synthase subunit a

ATP synthase subunit d, mitochondrial

ATP synthase subunit f, mitochondrial

ATP synthase subunit g, mitochondrial

ATP synthase subunit ATP5MPL, mitochondrial

ATP synthase F(0) complex subunit B1, mitochondrial

ATP synthase-coupling factor 6, mitochondrial

ATP synthase membrane subunit DAPIT, mitochondrial

ATP synthase subunit e, mitochondrial

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