SMTL ID : 8dbr.1

E. coli ATP synthase imaged in 10mM MgATP State2 "half-up

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: 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 F: R.343, D.346 Ligands: MG.2 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:T.176, A:A.177, A:E.331, A:R.365, A:Q.433, A:Q.435, F:R.343 Salt bridges: A:K.175, A:K.175, F:R.343 ATP.3: 17 residues within 4Å: Chain B: Y.150, R.171, Q.172, T.173, G.174, K.175, T.176, A.177, E.331, F.360, R.365, P.366, Q.433, Q.435 Chain D: R.343, Y.355 Ligands: MG.4 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.172, B:T.173, B:G.174, B:K.175, B:T.176, B:A.177, B:Q.433, B:Q.435 Salt bridges: B:K.175, B:K.175, D:R.343 ATP.5: 14 residues within 4Å: Chain C: 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 E: Y.355 Ligands: MG.6 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:Q.172, C:Q.172, C:T.173, C:T.173, C:G.174, C:K.175, C:T.176, C:A.177, C:R.365, C:Q.433, C:Q.435, C:Q.435, E:Y.355 Salt bridges: C:K.175, C:K.175 ATP.8: 19 residues within 4Å: Chain A: S.347, V.374, R.376 Chain D: G.151, A.152, G.153, G.155, K.156, T.157, V.158, E.182, R.183, Y.298, Y.332, F.405, A.408, F.411, T.412 Ligands: MG.7 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:G.153, D:G.155, D:K.156, D:T.157, D:T.157, D:T.157, D:V.158, D:R.183 Salt bridges: D:K.156, D:K.156, D:R.183, A:R.376, A:R.376, A:R.376 pi-Stacking: D:Y.332, D:Y.332

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.176 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.176 MG.4: 2 residues within 4Å: Chain B: T.176 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.176 MG.6: 2 residues within 4Å: Chain C: T.176 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.176 MG.7: 4 residues within 4Å: Chain D: T.157, E.182, R.183 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.157 MG.10: 3 residues within 4Å: Chain E: T.157, R.183 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.157

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

ADP.9: 15 residues within 4Å: Chain B: V.374, S.375, R.376 Chain E: G.153, V.154, G.155, K.156, T.157, V.158, Y.332, F.405, A.408, F.411, T.412 Ligands: MG.10 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:G.153, E:V.154, E:G.155, E:K.156, E:T.157, E:T.157, E:V.158, B:S.375, B:R.376 Salt bridges: E:K.156, B:R.376 pi-Stacking: E:Y.332, E:Y.332 ADP.11: 8 residues within 4Å: Chain F: G.153, G.155, K.156, T.157, V.158, Y.332, A.408, F.411 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.153, F:G.155, F:T.157, F:T.157, F:T.157 pi-Stacking: F:Y.332

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 alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H
ATP synthase subunit c: IJKLMNOPQR
ATP synthase subunit delta: S
ATP synthase subunit b: TU
ATP synthase subunit a: V

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
L

L
M

M
N

N
O

O
P

P
Q

Q
R

R
S

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 alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

ATP synthase subunit c

ATP synthase subunit delta

ATP synthase subunit b

ATP synthase subunit a

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