SMTL ID : 8f39.1

Yeast ATP synthase in conformation-2, at pH 6

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-10-1-1-1-1-3-3-1-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain T: R.170, Q.171, T.172, G.173, K.174, T.175, A.176, F.356, R.361, N.430, Q.431 Chain W: R.351, D.354 Ligands: MG.2 11 PLIP interactions: 7 interactions with chain T, 4 interactions with chain W Hydrogen bonds: T:R.170, T:G.173, T:G.173, T:A.176, T:Q.431, W:D.354, W:D.354 Salt bridges: T:K.174, W:R.351, W:R.351 pi-Cation interactions: T:R.361 ADP.3: 15 residues within 4Å: Chain U: Q.171, T.172, G.173, K.174, T.175, A.176, F.356, R.361, Q.429, N.430, Q.431 Chain X: S.350, R.351, L.353 Ligands: MG.4 11 PLIP interactions: 10 interactions with chain U, 1 interactions with chain X Hydrogen bonds: U:Q.171, U:T.172, U:G.173, U:T.175, U:A.176, U:Q.429, X:R.351 Salt bridges: U:K.174, U:K.174 pi-Cation interactions: U:R.361, U:R.361 ADP.5: 15 residues within 4Å: Chain V: R.170, Q.171, T.172, G.173, K.174, T.175, A.176, F.356, R.361, P.362, Q.429, N.430, Q.431 Chain Y: Y.363 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain V Hydrogen bonds: V:Q.171, V:T.172, V:G.173, V:K.174, V:T.175, V:A.176, V:E.327, V:Q.429, V:Q.431 Salt bridges: V:K.174, V:K.174 ADP.7: 20 residues within 4Å: Chain T: I.342, S.343, V.370, R.372 Chain X: G.153, A.154, G.155, V.156, G.157, K.158, T.159, V.160, R.185, E.188, Y.340, F.413, A.416, F.419, T.420 Ligands: MG.8 10 PLIP interactions: 8 interactions with chain X, 2 interactions with chain T Hydrogen bonds: X:G.155, X:G.157, X:K.158, X:T.159, X:E.188, T:R.372 Salt bridges: X:K.158, X:R.185, X:R.185, T:R.372 ADP.9: 17 residues within 4Å: Chain U: V.370, S.371, R.372 Chain Y: G.153, G.155, V.156, G.157, K.158, T.159, V.160, R.185, Y.340, P.341, F.413, A.416, F.419, T.420 15 PLIP interactions: 11 interactions with chain Y, 4 interactions with chain U Hydrogen bonds: Y:G.155, Y:V.156, Y:G.157, Y:K.158, Y:T.159, Y:T.159, Y:T.159, Y:V.160, U:S.371, U:R.372 Salt bridges: Y:K.158, Y:R.185, Y:R.185, U:R.372, U:R.372

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain T: T.175, D.268 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain U: T.175, D.268 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain V: T.175 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain X: T.159, E.184, R.185 Ligands: ADP.7 2 PLIP interactions: 2 interactions with chain X Metal complexes: X:E.184, X:E.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, S. et al., Conformational ensemble of yeast ATP synthase at low pH reveals unique intermediates and plasticity in F 1 -F o coupling. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-02-07

Peptides

ATP synthase subunit gamma, mitochondrial: A
ATP synthase subunit 4, mitochondrial: B
ATP synthase subunit d, mitochondrial: C
ATP synthase subunit H, mitochondrial: D
ATP synthase subunit f, mitochondrial: E
ATP synthase subunit 9, mitochondrial: FGHIJKLMNO
ATP synthase protein 8: P
ATP synthase subunit a: Q
ATP synthase subunit J, mitochondrial: R
ATP synthase subunit 5, mitochondrial: S
ATP synthase subunit alpha, mitochondrial: TUV
ATP synthase subunit beta, mitochondrial: WXY
ATP synthase subunit delta, mitochondrial: Z
ATP synthase subunit epsilon, mitochondrial: 0

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
Z

C
7

D
6

E
U

F
S

G
T

H
K

I
L

J
M

K
N

L
O

M
P

N
Q

O
R

P
8

Q
X

R
J

S
Y

T
A

U
B

V
C

W
D

X
E

Y
F

Z
H

0
I

Membrane

We predict this structure to be a membrane protein.
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ATP synthase subunit gamma, mitochondrial

ATP synthase subunit 4, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase subunit H, mitochondrial

ATP synthase subunit f, mitochondrial

ATP synthase subunit 9, mitochondrial

ATP synthase protein 8

ATP synthase subunit a

ATP synthase subunit J, mitochondrial

ATP synthase subunit 5, mitochondrial

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta, mitochondrial

ATP synthase subunit delta, mitochondrial

ATP synthase subunit epsilon, mitochondrial

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