SMTL ID : 8h9t.1

Human ATP synthase state 2 (combined)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 15 residues within 4Å: Chain T: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, Q.432 Chain X: S.358, Y.371 Ligands: MG.2 16 PLIP interactions: 14 interactions with chain T, 2 interactions with chain X Hydrogen bonds: T:Q.172, T:Q.172, T:T.173, T:T.173, T:G.174, T:K.175, T:T.176, T:S.177, T:S.177, T:Q.430, T:Q.432, X:S.358, X:Y.371 Salt bridges: T:K.175, T:K.175 pi-Stacking: T:F.357 ATP.3: 15 residues within 4Å: Chain 0: Y.371 Chain U: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, Q.432 Ligands: MG.4 16 PLIP interactions: 14 interactions with chain U, 2 interactions with chain 0 Hydrogen bonds: U:D.170, U:Q.172, U:Q.172, U:T.173, U:G.174, U:K.175, U:T.176, U:S.177, U:S.177, U:R.362, U:Q.430, U:Q.432, 0:S.358, 0:Y.371 Salt bridges: U:K.175, U:K.175 ATP.5: 15 residues within 4Å: Chain V: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, Q.432 Chain W: R.359, D.362 Ligands: MG.6 15 PLIP interactions: 12 interactions with chain V, 3 interactions with chain W Hydrogen bonds: V:Q.172, V:T.173, V:T.173, V:G.174, V:K.175, V:T.176, V:T.176, V:S.177, V:S.177, V:Q.430, W:R.359, W:D.362 Salt bridges: V:K.175, V:K.175, W:R.359

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain T: T.176 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:T.176 MG.4: 3 residues within 4Å: Chain U: T.176, D.269 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:T.176 MG.6: 3 residues within 4Å: Chain V: T.176, D.269 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:T.176 MG.8: 5 residues within 4Å: Chain X: K.165, T.166, E.191, D.259 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:T.166 MG.10: 4 residues within 4Å: Chain 0: T.166, E.191, R.192 Ligands: ADP.9 No protein-ligand interaction detected (PLIP)

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

ADP.7: 16 residues within 4Å: Chain V: 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, T.428 Ligands: MG.8 13 PLIP interactions: 10 interactions with chain X, 3 interactions with chain V Hydrogen bonds: X:G.160, X:G.162, X:V.163, X:G.164, X:K.165, X:T.166, X:V.167, X:R.192, V:R.373 Salt bridges: X:K.165, V:R.373, V:R.373 pi-Stacking: X:Y.348 ADP.9: 11 residues within 4Å: Chain 0: G.160, G.162, V.163, G.164, K.165, T.166, V.167, E.195 Chain T: V.371, R.373 Ligands: MG.10 13 PLIP interactions: 11 interactions with chain 0, 2 interactions with chain T Hydrogen bonds: 0:G.160, 0:G.160, 0:G.162, 0:V.163, 0:G.164, 0:K.165, 0:T.166, 0:T.166, 0:V.167 Salt bridges: 0:K.165, T:R.373, T:R.373 pi-Stacking: 0:Y.348

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 B1, mitochondrial: A
ATP synthase-coupling factor 6, mitochondrial: B
ATP synthase subunit d, mitochondrial: C
ATP synthase F(0) complex subunit C1, mitochondrial: DEFGHIJK
ATP synthase subunit delta, mitochondrial: L
ATP synthase subunit epsilon, mitochondrial: M
ATP synthase subunit a: N
ATP synthase subunit ATP5MJ, mitochondrial: O
ATP synthase subunit f, mitochondrial: P
ATP synthase subunit g, mitochondrial: Q
ATP synthase subunit e, mitochondrial: R
ATP synthase protein 8: S
ATP synthase subunit alpha, mitochondrial: TUV
ATP synthase subunit beta, mitochondrial: WX0
ATP synthase subunit gamma, mitochondrial: Y
ATP synthase subunit O, mitochondrial: Z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

D
6

E
7

F
8

G
1

H
2

I
3

J
4

K
5

L
H

M
I

N
N

O
P

P
R

Q
S

R
T

S
Q

T
C

U
A

V
B

W
E

X
F

0
D

Y
G

Z
O

Membrane

We predict this structure to be a membrane protein.
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ATP synthase F(0) complex subunit B1, mitochondrial

ATP synthase-coupling factor 6, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase F(0) complex subunit C1, mitochondrial

ATP synthase subunit delta, mitochondrial

ATP synthase subunit epsilon, mitochondrial

ATP synthase subunit a

ATP synthase subunit ATP5MJ, mitochondrial

ATP synthase subunit f, mitochondrial

ATP synthase subunit g, mitochondrial

ATP synthase subunit e, mitochondrial

ATP synthase protein 8

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta, mitochondrial

ATP synthase subunit gamma, mitochondrial

ATP synthase subunit O, mitochondrial

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