SMTL ID : 8dbp.1

E. coli ATP synthase imaged in 10mM MgATP State1 "half-up

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-3-3-1-1-1-2-1-mer

Ligands

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

ATP.1: 16 residues within 4Å: Chain K: R.171, Q.172, T.173, G.174, K.175, T.176, A.177, E.331, F.360, R.365, Q.433, K.434, Q.435 Chain P: R.354, Y.366 Ligands: MG.2 15 PLIP interactions: 4 interactions with chain P, 11 interactions with chain K Hydrogen bonds: P:Y.366, K:Q.172, K:T.173, K:G.174, K:K.175, K:T.176, K:A.177, K:E.331, K:Q.433, K:Q.435 Salt bridges: P:R.354, P:R.354, P:R.354, K:K.175, K:K.175 ATP.3: 15 residues within 4Å: Chain L: R.171, Q.172, T.173, G.174, K.175, T.176, A.177, F.360, R.365, Q.433, K.434, Q.435 Chain N: R.354, D.357 Ligands: MG.4 12 PLIP interactions: 10 interactions with chain L, 2 interactions with chain N Hydrogen bonds: L:Q.172, L:T.173, L:G.174, L:K.175, L:T.176, L:A.177, L:R.365, L:Q.433, N:R.354 Salt bridges: L:K.175, L:K.175, N:R.354 ATP.5: 18 residues within 4Å: Chain M: Y.150, R.171, Q.172, T.173, G.174, K.175, T.176, A.177, F.360, R.365, P.366, Q.433, K.434, Q.435 Chain O: R.354, D.357, Y.366 Ligands: MG.6 15 PLIP interactions: 2 interactions with chain O, 13 interactions with chain M Hydrogen bonds: O:Y.366, M:Y.150, M:Q.172, M:T.173, M:G.174, M:K.175, M:T.176, M:T.176, M:A.177, M:Q.433, M:Q.435, M:Q.435 Salt bridges: O:R.354, M:K.175, M:K.175 ATP.8: 17 residues within 4Å: Chain L: S.347, V.374, R.376 Chain O: G.164, V.165, G.166, K.167, T.168, V.169, E.193, R.194, E.197, Y.343, F.416, A.419, T.423 Ligands: MG.9 16 PLIP interactions: 13 interactions with chain O, 3 interactions with chain L Hydrogen bonds: O:G.164, O:V.165, O:G.166, O:K.167, O:T.168, O:T.168, O:T.168, O:V.169 Salt bridges: O:K.167, O:K.167, O:R.194, L:R.376, L:R.376, L:R.376 pi-Stacking: O:Y.343, O:Y.343

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain K: T.176 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.176 MG.4: 2 residues within 4Å: Chain L: T.176 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.176 MG.6: 2 residues within 4Å: Chain M: T.176 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.176 MG.9: 4 residues within 4Å: Chain O: K.167, T.168, E.193 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.168 MG.11: 4 residues within 4Å: Chain P: T.168, R.194, E.197 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.168

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

ADP.7: 10 residues within 4Å: Chain N: A.163, G.164, V.165, G.166, K.167, T.168, V.169, Y.343, A.419, F.422 9 PLIP interactions: 9 interactions with chain N Hydrogen bonds: N:G.164, N:V.165, N:G.166, N:K.167, N:T.168, N:V.169, N:Y.343 pi-Stacking: N:Y.343, N:Y.343 ADP.10: 14 residues within 4Å: Chain M: S.375, R.376 Chain P: G.162, A.163, G.164, V.165, G.166, K.167, T.168, V.169, Y.343, A.419, F.422 Ligands: MG.11 12 PLIP interactions: 10 interactions with chain P, 2 interactions with chain M Hydrogen bonds: P:G.164, P:V.165, P:G.166, P:K.167, P:T.168, P:T.168, P:V.169, M:S.375 Salt bridges: P:K.167, M:R.376 pi-Stacking: P:Y.343, P:Y.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sobti, M. et al., Changes within the central stalk of E. coli F 1 F o ATP synthase observed after addition of ATP. Commun Biol (2023)

Release Date

2023-01-25

Peptides

ATP synthase subunit c: ABCDEFGHIJ
ATP synthase subunit alpha: KLM
ATP synthase subunit beta: NOP
ATP synthase gamma chain: Q
ATP synthase epsilon chain: R
ATP synthase subunit delta: S
ATP synthase subunit b: TU
ATP synthase subunit a: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
L

D
M

E
N

F
O

G
P

H
Q

I
R

J
S

K
A

L
B

M
C

N
D

O
E

P
F

Q
G

R
H

S
W

T
X

U
Y

V
a

Membrane

We predict this structure to be a membrane protein.
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ATP synthase subunit c

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

ATP synthase subunit delta

ATP synthase subunit b

ATP synthase subunit a

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