SMTL ID : 8dbq.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: R.170, Q.171, T.172, G.173, K.174, T.175, A.176, E.330, F.359, R.364, Q.432, Q.434 Chain F: R.343, Y.355, R.359 Ligands: MG.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:Q.171, A:T.172, A:G.173, A:K.174, A:T.175, A:A.176, A:E.330, A:Q.432, A:Q.434 Salt bridges: A:K.174, A:K.174, F:R.343, F:R.343 ATP.3: 17 residues within 4Å: Chain B: Y.149, D.169, R.170, Q.171, T.172, G.173, K.174, T.175, A.176, F.359, R.364, Q.432, K.433, Q.434 Chain D: R.343, D.346 Ligands: MG.4 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Q.171, B:T.172, B:G.173, B:K.174, B:T.175, B:T.175, B:A.176, B:R.364, B:Q.432, D:R.343, D:D.346 Salt bridges: B:K.174, B:K.174, D:R.343 ATP.5: 16 residues within 4Å: Chain C: Y.149, D.169, Q.171, T.172, G.173, K.174, T.175, A.176, F.359, Q.432, K.433, Q.434 Chain E: R.343, D.346, Y.355 Ligands: MG.6 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:Q.171, C:T.172, C:T.172, C:G.173, C:K.174, C:T.175, C:T.175, C:A.176, C:Q.432, C:Q.434, C:Q.434, E:Y.355 Salt bridges: C:K.174, C:K.174, E:R.343 ATP.8: 17 residues within 4Å: Chain B: S.346, R.375 Chain E: G.151, G.153, V.154, G.155, K.156, T.157, V.158, E.182, R.183, E.186, Y.332, F.405, A.408, F.411 Ligands: MG.9 17 PLIP interactions: 4 interactions with chain B, 13 interactions with chain E Hydrogen bonds: B:S.346, E:G.153, E:V.154, E:G.155, E:K.156, E:T.157, E:T.157, E:V.158, E:E.186 Salt bridges: B:R.375, B:R.375, B:R.375, E:K.156, E:K.156, E:R.183 pi-Stacking: E:Y.332, E:Y.332

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.175 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.175 MG.4: 3 residues within 4Å: Chain B: T.175, Q.199 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.175 MG.6: 2 residues within 4Å: Chain C: T.175 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.175 MG.9: 5 residues within 4Å: Chain B: R.375 Chain E: T.157, R.183, E.186 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.157, E:E.186 MG.11: 4 residues within 4Å: Chain F: T.157, R.183, E.186 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.157

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

ADP.7: 10 residues within 4Å: Chain D: A.152, G.153, V.154, G.155, K.156, T.157, V.158, Y.332, A.408, F.411 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.153, D:V.154, D:G.155, D:K.156, D:T.157, D:Y.332 pi-Stacking: D:Y.332, D:Y.332 ADP.10: 15 residues within 4Å: Chain C: S.374, R.375 Chain F: G.151, A.152, G.153, V.154, G.155, K.156, T.157, V.158, Y.332, F.405, A.408, F.411 Ligands: MG.11 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:G.153, F:V.154, F:G.155, F:K.156, F:T.157, F:T.157, F:V.158, C:S.374 Salt bridges: F:K.156, C:R.375 pi-Stacking: F:Y.332, 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: AC
ATP synthase subunit alpha: B
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

C
C

B
B

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 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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