SMTL ID : 8dbt.1

E. coli ATP synthase imaged in 10mM MgATP State2 "down

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-10-2-1-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.354, D.357 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.354 Salt bridges: A:K.175, A:K.175, F:R.354 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.354, Y.366 Ligands: MG.4 12 PLIP interactions: 11 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, B:Q.435 Salt bridges: B:K.175, B:K.175, D:R.354 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.366 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.150, C:Q.172, C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:A.177, C:Q.433, C:Q.435, C:Q.435 Salt bridges: C:K.175, C:K.175 ATP.8: 18 residues within 4Å: Chain A: S.347, V.374, R.376 Chain D: A.163, G.164, V.165, G.166, K.167, T.168, V.169, E.193, R.194, Y.343, F.416, A.419, F.422, T.423 Ligands: MG.7 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:G.162, D:G.164, D:V.165, D:G.166, D:K.167, D:T.168, D:T.168, D:V.169, A:S.347, A:S.347 Salt bridges: D:K.167, D:K.167, D:R.194, A:R.376, A:R.376, A:R.376 pi-Stacking: D:Y.343, D:Y.343

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: 3 residues within 4Å: Chain C: T.176, Q.200 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.176 MG.7: 3 residues within 4Å: Chain D: T.168, E.193 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.168 MG.10: 3 residues within 4Å: Chain E: K.167, T.168 Ligands: ADP.9 No protein-ligand interaction detected (PLIP)

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.164, V.165, G.166, K.167, T.168, V.169, Y.343, F.416, A.419, F.422, T.423 Ligands: MG.10 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:G.164, E:V.165, E:G.166, E:K.167, E:T.168, E:T.168, E:V.169, B:S.375, B:R.376 Salt bridges: E:K.167, B:R.376 pi-Stacking: E:Y.343, E:Y.343 ADP.11: 9 residues within 4Å: Chain F: G.164, G.166, K.167, T.168, V.169, Y.343, Q.414, A.419, F.422 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:G.164, F:G.166, F:K.167, F:T.168, F:T.168, F:V.169, F:Q.414, F:F.416 pi-Stacking: F: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 alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H
ATP synthase subunit delta: I
ATP synthase subunit c: JKLMNOPQRS
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
W

J
I

K
J

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

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 delta

ATP synthase subunit c

ATP synthase subunit b

ATP synthase subunit a

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