SMTL ID : 8h9v.1

Human ATP synthase state 3b (combined)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 14 residues within 4Å: Chain T: 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 Y: R.359 Ligands: MG.2 15 PLIP interactions: 13 interactions with chain T, 2 interactions with chain Y Hydrogen bonds: T:D.170, T:Q.172, T:T.173, T:G.174, T:K.175, T:T.176, T:T.176, T:S.177, T:S.177, T:Q.430, T:Q.432 Salt bridges: T:K.175, T:K.175, Y:R.359, Y:R.359 ATP.3: 16 residues within 4Å: Chain U: 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 W: R.359, D.362 Ligands: MG.4 18 PLIP interactions: 15 interactions with chain U, 3 interactions with chain W Hydrogen bonds: U:Q.172, U:T.173, U:G.174, U:K.175, U:T.176, U:T.176, U:S.177, U:S.177, U:S.177, U:Q.430, U:Q.432, W:R.359, W:D.362 Salt bridges: U:K.175, U:K.175, W:R.359 pi-Stacking: U:F.357 pi-Cation interactions: U:R.362 ATP.5: 14 residues within 4Å: Chain V: 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 X: Y.371 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain V Hydrogen bonds: V:Q.172, V:T.173, V:G.174, V:K.175, V:T.176, V:T.176, V:T.176, V:S.177, V:S.177, V:Q.430, V:Q.432 Salt bridges: V:K.175, V:K.175 pi-Stacking: V:F.357

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain T: T.176, D.269 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain T Metal complexes: T:T.176, T:D.269 MG.4: 4 residues within 4Å: Chain U: T.176, Q.208, D.269 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:T.176 MG.6: 4 residues within 4Å: Chain V: T.176, Q.208, D.269 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:T.176, V:D.269 MG.8: 4 residues within 4Å: Chain X: T.166, E.191, D.259 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:T.166 MG.10: 5 residues within 4Å: Chain Y: N.260, I.261, F.262, A.312 Ligands: ADP.9 No protein-ligand interaction detected (PLIP)

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

ADP.7: 15 residues within 4Å: Chain U: V.371, R.373 Chain X: G.160, G.162, V.163, G.164, K.165, T.166, V.167, R.192, Y.348, F.421, A.424, F.427 Ligands: MG.8 14 PLIP interactions: 11 interactions with chain X, 3 interactions with chain U Hydrogen bonds: X:G.162, X:V.163, X:G.164, X:K.165, X:T.166, X:T.166, X:T.166, X:V.167, U:R.373 Salt bridges: X:K.165, X:R.192, U:R.373, U:R.373 pi-Stacking: X:Y.348 ADP.9: 14 residues within 4Å: Chain V: R.373 Chain Y: G.156, L.157, F.158, G.159, G.160, G.162, K.165, E.195, N.260, Q.311, A.312, L.332 Ligands: MG.10 3 PLIP interactions: 2 interactions with chain Y, 1 interactions with chain V Hydrogen bonds: Y:K.165, Y:E.195, V:R.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lai, Y. et al., Structure of the human ATP synthase. Mol.Cell (2023)

Release Date

2023-05-31

Peptides

ATP synthase F(0) complex subunit C1, mitochondrial: ABCDEFGH
ATP synthase subunit delta, mitochondrial: I
ATP synthase subunit epsilon, mitochondrial: J
ATP synthase F(0) complex subunit B1, mitochondrial: K
ATP synthase subunit d, mitochondrial: L
ATP synthase subunit a: M
ATP synthase subunit ATP5MJ, mitochondrial: N
ATP synthase protein 8: O
ATP synthase subunit f, mitochondrial: P
ATP synthase subunit g, mitochondrial: Q
ATP synthase subunit e, mitochondrial: R
ATP synthase-coupling factor 6, mitochondrial: S
ATP synthase subunit alpha, mitochondrial: TUV
ATP synthase subunit beta, mitochondrial: WXY
ATP synthase subunit gamma, mitochondrial: Z
ATP synthase subunit O, mitochondrial: 0

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
4

B
5

C
6

D
7

E
8

F
1

G
2

H
3

I
H

J
I

K
K

L
M

M
N

N
P

O
Q

P
R

Q
S

R
T

S
L

T
A

U
B

V
C

W
E

X
F

Y
D

Z
G

0
O

Membrane

We predict this structure to be a membrane protein.
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ATP synthase F(0) complex subunit C1, mitochondrial

ATP synthase subunit delta, mitochondrial

ATP synthase subunit epsilon, mitochondrial

ATP synthase F(0) complex subunit B1, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase subunit a

ATP synthase subunit ATP5MJ, mitochondrial

ATP synthase protein 8

ATP synthase subunit f, mitochondrial

ATP synthase subunit g, mitochondrial

ATP synthase subunit e, mitochondrial

ATP synthase-coupling factor 6, mitochondrial

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta, mitochondrial

ATP synthase subunit gamma, mitochondrial

ATP synthase subunit O, mitochondrial

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